[BioC] Reading ArrayExpress data [was Re: questions on the ImaGene data using limma package]

Ming YI [Contr] myi at ncifcrf.gov
Thu Oct 30 22:28:17 CET 2008


Dear Gordon:

Thanks a lot for your comments and suggestions. I already 
successfully read all the data into limma objects based on your 
suggestion using the generic method by using the attached target file 
I edited from their annotation file as I sent to you earlier. I did 
assume that the Cy3 channel is the common reference as you guessed.

But the issue remained as you mentioned how actually they did the 
experiment. Based on their E-NCMF-8.idf.txt file from 
arrayExpress,  it appears to be dye_swap_design, which is exactly 
what you guessed. So the data appears to be collated by ArrayExpress 
into data matrices with the Cy3 and Cy5 intensities in the same file 
for each sample. But the concern is in the column of "Label" in the 
file E-NCMF-8_sdrf.txt  I sent to you in last email, what does those 
Cy3 and Cy5 mean for each sample, it looks like this column may tell 
for each sample (and corresponding raw data file), what is dye for 
the sample and the other dye would be used for the common reference, 
which was not mentioned in their annotation file. What do you think? 
if this is true, I may need to change my target file coordinately to 
accommodate this information. This assumption makes more sense at 
least to explain the repeated samples in the dataset, which should be 
the dye-swapping data.

I tried to contact with them for details of the experiment design, 
that should help to sort this out.

By the way, I am not sure why my post not go to the mailing list. I 
changed a bit the address this time, hope it works.

Thanks again for your help. Any additional suggestion would be 
appreciated as well.

Best regards,

Ming


At 09:25 PM 10/29/2008, Gordon K Smyth wrote:
>Dear Ming,
>
>Thank you for mailing me example data sets and the annotation 
>spreadsheet from ArrayExpress.
>
>You are assuming that the data from ArrayExpress are in ImaGene 
>format. This is incorrect.  The reason that limma gives a special 
>treatment to ImaGene files is that, unlike other image analysis 
>software, ImaGene writes the Cy3 and Cy5 channels into separate 
>files.  However ArrayExpress has collated the original data into 
>data matrices with the Cy3 and Cy5 intensities in the same file for 
>each sample.  Therefore you should ignore all references to ImaGene 
>in the limma manual, and instead use the instructions for generic 
>two-color platforms.
>
>The data sets you sent me can easily be read into limma using the 
>instructions in the limma User's Guide starting page 14 "What should 
>you do if your image analysis program is not in the above list?"  I 
>demonstrate this below.
>
>Your emails suggest that you have not yet read any two-color data 
>into limma.  It is essential that you try some simple examples 
>before trying a large dataset from ArrayExpress, which will have a 
>complex structure you might not fully understand.
>
>I don't fully understand the sample annotation file from 
>ArrayExpress that you sent me, but I doubt that you are 
>interpretting it correctly.  It is not in the format you need for a 
>limma targets file.  My guess is that each row of the file 
>corresponds to one array, and that each array has been hybridized 
>with a common reference that is not mentioned in the annotation 
>file.  This means that the repeated sample names you have noted do 
>not represent matched Cy3 and Cy5 channels, but rather represent 
>dye-swap technical replicates.  That is, they are separate arrays.
>
>If my guess is correct, then a targets file would be something like below.
>
>Let me emphasize that I do not offer a plug-in service to read 
>experimental data posted to ArrayExpress.  It is your responsibility 
>to figure out the experimental design and the ArrayExpression data 
>formats. I am just guessing.
>
>Best wishes
>Gordon
>
>
>READING YOUR DATA FILES
>
>>f
>[1] "E-NCMF-8-raw-data-1363346838.txt" "E-NCMF-8-raw-data-1363346856.txt"
>
>>ann <- c("Database NCMF:DB:omadhuman","Database
>ebi.ac.uk:Database:ens_trscrpt_id","Feature coordinates: 
>metaColumn","metaRow","column","row","Reporter identifier","Reporter 
>sequence type")
>
>>columns <- list(Rf="ImaGene:Signal Mean_Cy5",Rb="ImaGene:Background
>Median_Cy5",Gf="ImaGene:Signal Mean_Cy3",Gb="ImaGene:Background Median_Cy3")
>
>>RG <- read.maimages(files=f,annotation=ann,columns=columns)
>Read E-NCMF-8-raw-data-1363346838.txt
>Read E-NCMF-8-raw-data-1363346856.txt
>
>>dim(RG)
>[1] 37632     2
>
>
>A POSSIBLE TARGETS FILE
>
>>targets <- readTargets()
>>targets
>                       Source            DiseaseState 
> ArrayDataMatrixFile       Cy3       Cy5
>1                       3560 Squamous Cell Carcinoma 
>E-NCMF-8-raw-data-1363346838.txt Reference   SCC3560
>2 reference pool of 61 HNSCC Squamous Cell Carcinoma 
>E-NCMF-8-raw-data-1363346856.txt Reference PoolHNSCC
>
>
>On Wed, 29 Oct 2008, Ming YI [Contr] wrote:
>
>>Hi, Dear Gordon:
>>
>>I tried to use limma to deal with ImaGene dataset I downloaded from 
>>ArrayExpress. I never deal with ImaGene data before and not 
>>familiar with ImaGene data format except knowing that the Cy5 and 
>>Cy3 signals are stored in two separate files for the same sample. I 
>>tried to read the data into limma and normalize them in the context 
>>of limma. and I keep running into issues and errors. and I wish you 
>>can help me with this regard:
>>
>>I did attach a file (E-NCMF-8_sdrf.txt) that was download from 
>>ArrayExpress can be potentially used for making the target file, 
>>and also I attached two raw data files of the ImaGene dataset as 
>>examples. The thing bothering me is as followed:
>>
>>Extract 3538  and Extract 3526 (see column "Extract Name" of 
>>E-NCMF-8_sdrf.txt file) , they do have one Cy5 and one matched Cy3 
>>files, so that's fine with me. but in particular, for "Extract 
>>reference pool of 61 HNSCC" (see E-NCMF-8_sdrf.txt file), there are 
>>multiple Cy3 and Cy5 for such samples, how should we incorporate 
>>that into the target file?
>>
>>I intended to use the following code to deal with this ImaGene data
>>
>>targets<-readTargets()
>>files<-targets[,c("FileNameCy3", "FileNameCy5")'
>>RG<-read.maimages(files, source="imagene")
>>
>>but I need the right target file to start with particularly with 
>>the issue I mentioned above.
>>
>>Also for normalization, the
>>RG<-backgroundCorrect(RG, method="normexp", offset=50) still 
>>appropiate for ImaGene data?
>>
>>Thanks so much for your help!
>>
>>Ming Yi
>>ABCC
>>P.O.Box B, Bldg 430
>>National Cancer Institute/SAIC-Frederick, Inc
>>Frederick,Maryland
>>USA
-------------- next part --------------
Name	SourceName	DiseaseState	DiseaseOutcome	OrganismPart	Extract Name	LabeledExtract Name	Label	FactorValue_treatment	ArrayDataMatrixFile	Cy3	Cy5
NCMF1363348819	2876	Squamous Cell Carcinoma	locoregional recurrence	oropharynx	Extract 2876	Labeled Extract 2876	Cy3	cisplatin-based chemoradiation (RADPLAT)	E-NCMF-8-raw-data-1363348819.txt	Ref	cisplatin-based chemoradiation (RADPLAT)
NCMF1363347883	3374	Squamous Cell Carcinoma	locoregional recurrence	oral cavity	Extract 3374	Labeled Extract 3374	Cy3	cisplatin-based chemoradiation (RADPLAT)	E-NCMF-8-raw-data-1363347883.txt	Ref	cisplatin-based chemoradiation (RADPLAT)
NCMF1363347847	3376	Squamous Cell Carcinoma	locoregional recurrence	oropharynx	Extract 3376	Labeled Extract 3376	Cy3	cisplatin-based chemoradiation (RADPLAT)	E-NCMF-8-raw-data-1363347847.txt	Ref	cisplatin-based chemoradiation (RADPLAT)
NCMF1363347775	3378	Squamous Cell Carcinoma	locoregional recurrence	oropharynx	Extract 3378	Labeled Extract 3378	Cy5	cisplatin-based chemoradiation (RADPLAT)	E-NCMF-8-raw-data-1363347775.txt	Ref	cisplatin-based chemoradiation (RADPLAT)
NCMF1363347829	3378	Squamous Cell Carcinoma	locoregional recurrence	oropharynx	Extract 3378	Labeled Extract 3378	Cy3	cisplatin-based chemoradiation (RADPLAT)	E-NCMF-8-raw-data-1363347829.txt	Ref	cisplatin-based chemoradiation (RADPLAT)
NCMF1363347649	3497	Squamous Cell Carcinoma	"cured, no recurrence"	oropharynx	Extract 3497	Labeled Extract 3497	Cy3	cisplatin-based chemoradiation (RADPLAT)	E-NCMF-8-raw-data-1363347649.txt	Ref	cisplatin-based chemoradiation (RADPLAT)
NCMF1363347685	3497	Squamous Cell Carcinoma	"cured, no recurrence"	oropharynx	Extract 3497	Labeled Extract 3497	Cy5	cisplatin-based chemoradiation (RADPLAT)	E-NCMF-8-raw-data-1363347685.txt	Ref	cisplatin-based chemoradiation (RADPLAT)
NCMF1363347613	3502	Squamous Cell Carcinoma	"cured, no recurrence"	oropharynx	Extract 3502	Labeled Extract 3502	Cy5	cisplatin-based chemoradiation (RADPLAT)	E-NCMF-8-raw-data-1363347613.txt	Ref	cisplatin-based chemoradiation (RADPLAT)
NCMF1363347667	3502	Squamous Cell Carcinoma	"cured, no recurrence"	oropharynx	Extract 3502	Labeled Extract 3502	Cy3	cisplatin-based chemoradiation (RADPLAT)	E-NCMF-8-raw-data-1363347667.txt	Ref	cisplatin-based chemoradiation (RADPLAT)
NCMF1363349251	3504	Squamous Cell Carcinoma	"cured, no recurrence"	oropharynx	Extract 3504	Labeled Extract 3504	Cy3	cisplatin-based chemoradiation (RADPLAT)	E-NCMF-8-raw-data-1363349251.txt	Ref	cisplatin-based chemoradiation (RADPLAT)
NCMF1363349269	3504	Squamous Cell Carcinoma	"cured, no recurrence"	oropharynx	Extract 3504	Labeled Extract 3504	Cy5	cisplatin-based chemoradiation (RADPLAT)	E-NCMF-8-raw-data-1363349269.txt	Ref	cisplatin-based chemoradiation (RADPLAT)
NCMF1363347505	3509	Squamous Cell Carcinoma	"cured, no recurrence"	oropharynx	Extract 3509	Labeled Extract 3509	Cy3	cisplatin-based chemoradiation (RADPLAT)	E-NCMF-8-raw-data-1363347505.txt	Ref	cisplatin-based chemoradiation (RADPLAT)
NCMF1363347559	3509	Squamous Cell Carcinoma	"cured, no recurrence"	oropharynx	Extract 3509	Labeled Extract 3509	Cy5	cisplatin-based chemoradiation (RADPLAT)	E-NCMF-8-raw-data-1363347559.txt	Ref	cisplatin-based chemoradiation (RADPLAT)
NCMF1363347523	3512	Squamous Cell Carcinoma	"cured, no recurrence"	oropharynx	Extract 3512	Labeled Extract 3512	Cy5	cisplatin-based chemoradiation (RADPLAT)	E-NCMF-8-raw-data-1363347523.txt	Ref	cisplatin-based chemoradiation (RADPLAT)
NCMF1363347451	3513	Squamous Cell Carcinoma	locoregional recurrence	oropharynx	Extract 3513	Labeled Extract 3513	Cy5	cisplatin-based chemoradiation (RADPLAT)	E-NCMF-8-raw-data-1363347451.txt	Ref	cisplatin-based chemoradiation (RADPLAT)
NCMF1363347469	3513	Squamous Cell Carcinoma	locoregional recurrence	oropharynx	Extract 3513	Labeled Extract 3513	Cy3	cisplatin-based chemoradiation (RADPLAT)	E-NCMF-8-raw-data-1363347469.txt	Ref	cisplatin-based chemoradiation (RADPLAT)
NCMF1363347415	3514	Squamous Cell Carcinoma	locoregional recurrence	oropharynx	Extract 3514	Labeled Extract 3514	Cy3	cisplatin-based chemoradiation (RADPLAT)	E-NCMF-8-raw-data-1363347415.txt	Ref	cisplatin-based chemoradiation (RADPLAT)
NCMF1363347361	3516	Squamous Cell Carcinoma	locoregional recurrence	hypopharynx	Extract 3516	Labeled Extract 3516	Cy3	cisplatin-based chemoradiation (RADPLAT)	E-NCMF-8-raw-data-1363347361.txt	Ref	cisplatin-based chemoradiation (RADPLAT)
NCMF1363347397	3516	Squamous Cell Carcinoma	locoregional recurrence	hypopharynx	Extract 3516	Labeled Extract 3516	Cy5	cisplatin-based chemoradiation (RADPLAT)	E-NCMF-8-raw-data-1363347397.txt	Ref	cisplatin-based chemoradiation (RADPLAT)
NCMF1363347307	3518	Squamous Cell Carcinoma	"cured, no recurrence"	hypopharynx	Extract 3518	Labeled Extract 3518	Cy3	cisplatin-based chemoradiation (RADPLAT)	E-NCMF-8-raw-data-1363347307.txt	Ref	cisplatin-based chemoradiation (RADPLAT)
NCMF1363347198	3521	Squamous Cell Carcinoma	locoregional recurrence	oropharynx	Extract 3521	Labeled Extract 3521	Cy5	cisplatin-based chemoradiation (RADPLAT)	E-NCMF-8-raw-data-1363347198.txt	Ref	cisplatin-based chemoradiation (RADPLAT)
NCMF1363347253	3523	Squamous Cell Carcinoma	locoregional recurrence	oropharynx	Extract 3523	Labeled Extract 3523	Cy3	cisplatin-based chemoradiation (RADPLAT)	E-NCMF-8-raw-data-1363347253.txt	Ref	cisplatin-based chemoradiation (RADPLAT)
NCMF1363347126	3526	Squamous Cell Carcinoma	locoregional recurrence	oropharynx	Extract 3526	Labeled Extract 3526	Cy3	cisplatin-based chemoradiation (RADPLAT)	E-NCMF-8-raw-data-1363347126.txt	Ref	cisplatin-based chemoradiation (RADPLAT)
NCMF1363347144	3526	Squamous Cell Carcinoma	locoregional recurrence	oropharynx	Extract 3526	Labeled Extract 3526	Cy5	cisplatin-based chemoradiation (RADPLAT)	E-NCMF-8-raw-data-1363347144.txt	Ref	cisplatin-based chemoradiation (RADPLAT)
NCMF1363349683	3530	Squamous Cell Carcinoma	"cured, no recurrence"	oral cavity	Extract 3530	Labeled Extract 3530	Cy5	cisplatin-based chemoradiation (RADPLAT)	E-NCMF-8-raw-data-1363349683.txt	Ref	cisplatin-based chemoradiation (RADPLAT)
NCMF1363349647	3537	Squamous Cell Carcinoma	"cured, no recurrence"	hypopharynx	Extract 3537	Labeled Extract 3537	Cy3	cisplatin-based chemoradiation (RADPLAT)	E-NCMF-8-raw-data-1363349647.txt	Ref	cisplatin-based chemoradiation (RADPLAT)
NCMF1363347090	3538	Squamous Cell Carcinoma	"cured, no recurrence"	oropharynx	Extract 3538	Labeled Extract 3538	Cy3	cisplatin-based chemoradiation (RADPLAT)	E-NCMF-8-raw-data-1363347090.txt	Ref	cisplatin-based chemoradiation (RADPLAT)
NCMF1363347108	3538	Squamous Cell Carcinoma	"cured, no recurrence"	oropharynx	Extract 3538	Labeled Extract 3538	Cy5	cisplatin-based chemoradiation (RADPLAT)	E-NCMF-8-raw-data-1363347108.txt	Ref	cisplatin-based chemoradiation (RADPLAT)
NCMF1363347054	3539	Squamous Cell Carcinoma	"cured, no recurrence"	oropharynx	Extract 3539	Labeled Extract 3539	Cy3	cisplatin-based chemoradiation (RADPLAT)	E-NCMF-8-raw-data-1363347054.txt	Ref	cisplatin-based chemoradiation (RADPLAT)
NCMF1363348855	3540	Squamous Cell Carcinoma	"cured, no recurrence"	hypopharynx	Extract 3540	Labeled Extract 3540	Cy5	cisplatin-based chemoradiation (RADPLAT)	E-NCMF-8-raw-data-1363348855.txt	Ref	cisplatin-based chemoradiation (RADPLAT)
NCMF1363348873	3540	Squamous Cell Carcinoma	"cured, no recurrence"	hypopharynx	Extract 3540	Labeled Extract 3540	Cy3	cisplatin-based chemoradiation (RADPLAT)	E-NCMF-8-raw-data-1363348873.txt	Ref	cisplatin-based chemoradiation (RADPLAT)
NCMF1363347036	3541	Squamous Cell Carcinoma	"cured, no recurrence"	oropharynx	Extract 3541	Labeled Extract 3541	Cy5	cisplatin-based chemoradiation (RADPLAT)	E-NCMF-8-raw-data-1363347036.txt	Ref	cisplatin-based chemoradiation (RADPLAT)
NCMF1363349827	3542	Squamous Cell Carcinoma	"cured, no recurrence"	larynx	Extract 3542	Labeled Extract 3542	Cy5	cisplatin-based chemoradiation (RADPLAT)	E-NCMF-8-raw-data-1363349827.txt	Ref	cisplatin-based chemoradiation (RADPLAT)
NCMF1363349863	3542	Squamous Cell Carcinoma	"cured, no recurrence"	larynx	Extract 3542	Labeled Extract 3542	Cy3	cisplatin-based chemoradiation (RADPLAT)	E-NCMF-8-raw-data-1363349863.txt	Ref	cisplatin-based chemoradiation (RADPLAT)
NCMF1363347721	3544	Squamous Cell Carcinoma	locoregional recurrence	oropharynx	Extract 3544	Labeled Extract 3544	Cy5	cisplatin-based chemoradiation (RADPLAT)	E-NCMF-8-raw-data-1363347721.txt	Ref	cisplatin-based chemoradiation (RADPLAT)
NCMF1363346982	3548	Squamous Cell Carcinoma	locoregional recurrence	oropharynx	Extract 3548	Labeled Extract 3548	Cy3	cisplatin-based chemoradiation (RADPLAT)	E-NCMF-8-raw-data-1363346982.txt	Ref	cisplatin-based chemoradiation (RADPLAT)
NCMF1363347595	3559	Squamous Cell Carcinoma	locoregional recurrence	hypopharynx	Extract 3559	Labeled Extract 3559	Cy3	cisplatin-based chemoradiation (RADPLAT)	E-NCMF-8-raw-data-1363347595.txt	Ref	cisplatin-based chemoradiation (RADPLAT)
NCMF1363347631	3559	Squamous Cell Carcinoma	locoregional recurrence	hypopharynx	Extract 3559	Labeled Extract 3559	Cy5	cisplatin-based chemoradiation (RADPLAT)	E-NCMF-8-raw-data-1363347631.txt	Ref	cisplatin-based chemoradiation (RADPLAT)
NCMF1363346838	3560	Squamous Cell Carcinoma	"cured, no recurrence"	oropharynx	Extract 3560	Labeled Extract 3560	Cy5	cisplatin-based chemoradiation (RADPLAT)	E-NCMF-8-raw-data-1363346838.txt	Ref	cisplatin-based chemoradiation (RADPLAT)
NCMF1363348765	3561	Squamous Cell Carcinoma	"cured, no recurrence"	oropharynx	Extract 3561	Labeled Extract 3561	Cy5	cisplatin-based chemoradiation (RADPLAT)	E-NCMF-8-raw-data-1363348765.txt	Ref	cisplatin-based chemoradiation (RADPLAT)
NCMF1363349737	3562	Squamous Cell Carcinoma	"cured, no recurrence"	oropharynx	Extract 3562	Labeled Extract 3562	Cy3	cisplatin-based chemoradiation (RADPLAT)	E-NCMF-8-raw-data-1363349737.txt	Ref	cisplatin-based chemoradiation (RADPLAT)
NCMF1363348801	3563	Squamous Cell Carcinoma	"cured, no recurrence"	oropharynx	Extract 3563	Labeled Extract 3563	Cy5	cisplatin-based chemoradiation (RADPLAT)	E-NCMF-8-raw-data-1363348801.txt	Ref	cisplatin-based chemoradiation (RADPLAT)
NCMF1363346928	3564	Squamous Cell Carcinoma	"cured, no recurrence"	oropharynx	Extract 3564	Labeled Extract 3564	Cy3	cisplatin-based chemoradiation (RADPLAT)	E-NCMF-8-raw-data-1363346928.txt	Ref	cisplatin-based chemoradiation (RADPLAT)
NCMF1363346892	3573	Squamous Cell Carcinoma	"cured, no recurrence"	oropharynx	Extract 3573	Labeled Extract 3573	Cy3	cisplatin-based chemoradiation (RADPLAT)	E-NCMF-8-raw-data-1363346892.txt	Ref	cisplatin-based chemoradiation (RADPLAT)
NCMF1363347289	3574	Squamous Cell Carcinoma	"cured, no recurrence"	oropharynx	Extract 3574	Labeled Extract 3574	Cy3	cisplatin-based chemoradiation (RADPLAT)	E-NCMF-8-raw-data-1363347289.txt	Ref	cisplatin-based chemoradiation (RADPLAT)
NCMF1363349575	3575	Squamous Cell Carcinoma	"cured, no recurrence"	hypopharynx	Extract 3575	Labeled Extract 3575	Cy3	cisplatin-based chemoradiation (RADPLAT)	E-NCMF-8-raw-data-1363349575.txt	Ref	cisplatin-based chemoradiation (RADPLAT)
NCMF1363349629	3575	Squamous Cell Carcinoma	"cured, no recurrence"	hypopharynx	Extract 3575	Labeled Extract 3575	Cy5	cisplatin-based chemoradiation (RADPLAT)	E-NCMF-8-raw-data-1363349629.txt	Ref	cisplatin-based chemoradiation (RADPLAT)
NCMF1363347937	3589	Squamous Cell Carcinoma	"cured, no recurrence"	hypopharynx	Extract 3589	Labeled Extract 3589	Cy3	cisplatin-based chemoradiation (RADPLAT)	E-NCMF-8-raw-data-1363347937.txt	Ref	cisplatin-based chemoradiation (RADPLAT)
NCMF1363347991	3590	Squamous Cell Carcinoma	"cured, no recurrence"	oral cavity	Extract 3590	Labeled Extract 3590	Cy5	cisplatin-based chemoradiation (RADPLAT)	E-NCMF-8-raw-data-1363347991.txt	Ref	cisplatin-based chemoradiation (RADPLAT)
NCMF1363348009	3590	Squamous Cell Carcinoma	"cured, no recurrence"	oral cavity	Extract 3590	Labeled Extract 3590	Cy3	cisplatin-based chemoradiation (RADPLAT)	E-NCMF-8-raw-data-1363348009.txt	Ref	cisplatin-based chemoradiation (RADPLAT)
NCMF1363348027	3592	Squamous Cell Carcinoma	"cured, no recurrence"	oropharynx	Extract 3592	Labeled Extract 3592	Cy3	cisplatin-based chemoradiation (RADPLAT)	E-NCMF-8-raw-data-1363348027.txt	Ref	cisplatin-based chemoradiation (RADPLAT)
NCMF1363348063	3592	Squamous Cell Carcinoma	"cured, no recurrence"	oropharynx	Extract 3592	Labeled Extract 3592	Cy5	cisplatin-based chemoradiation (RADPLAT)	E-NCMF-8-raw-data-1363348063.txt	Ref	cisplatin-based chemoradiation (RADPLAT)
NCMF1363348045	3593	Squamous Cell Carcinoma	"cured, no recurrence"	oropharynx	Extract 3593	Labeled Extract 3593	Cy3	cisplatin-based chemoradiation (RADPLAT)	E-NCMF-8-raw-data-1363348045.txt	Ref	cisplatin-based chemoradiation (RADPLAT)
NCMF1363348117	3595	Squamous Cell Carcinoma	"cured, no recurrence"	oropharynx	Extract 3595	Labeled Extract 3595	Cy5	cisplatin-based chemoradiation (RADPLAT)	E-NCMF-8-raw-data-1363348117.txt	Ref	cisplatin-based chemoradiation (RADPLAT)
NCMF1363348207	3598	Squamous Cell Carcinoma	"cured, no recurrence"	hypopharynx	Extract 3598	Labeled Extract 3598	Cy3	cisplatin-based chemoradiation (RADPLAT)	E-NCMF-8-raw-data-1363348207.txt	Ref	cisplatin-based chemoradiation (RADPLAT)
NCMF1363348225	3598	Squamous Cell Carcinoma	"cured, no recurrence"	hypopharynx	Extract 3598	Labeled Extract 3598	Cy5	cisplatin-based chemoradiation (RADPLAT)	E-NCMF-8-raw-data-1363348225.txt	Ref	cisplatin-based chemoradiation (RADPLAT)
NCMF1363348243	3599	Squamous Cell Carcinoma	"cured, no recurrence"	hypopharynx	Extract 3599	Labeled Extract 3599	Cy5	cisplatin-based chemoradiation (RADPLAT)	E-NCMF-8-raw-data-1363348243.txt	Ref	cisplatin-based chemoradiation (RADPLAT)
NCMF1363348279	3600	Squamous Cell Carcinoma	locoregional recurrence	oral cavity	Extract 3600	Labeled Extract 3600	Cy3	cisplatin-based chemoradiation (RADPLAT)	E-NCMF-8-raw-data-1363348279.txt	Ref	cisplatin-based chemoradiation (RADPLAT)
NCMF1363348333	3603	Squamous Cell Carcinoma	"cured, no recurrence"	hypopharynx	Extract 3603	Labeled Extract 3603	Cy3	cisplatin-based chemoradiation (RADPLAT)	E-NCMF-8-raw-data-1363348333.txt	Ref	cisplatin-based chemoradiation (RADPLAT)
NCMF1363348423	3609	Squamous Cell Carcinoma	"cured, no recurrence"	oropharynx	Extract 3609	Labeled Extract 3609	Cy5	cisplatin-based chemoradiation (RADPLAT)	E-NCMF-8-raw-data-1363348423.txt	Ref	cisplatin-based chemoradiation (RADPLAT)
NCMF1363348495	3613	Squamous Cell Carcinoma	"cured, no recurrence"	oropharynx	Extract 3613	Labeled Extract 3613	Cy5	cisplatin-based chemoradiation (RADPLAT)	E-NCMF-8-raw-data-1363348495.txt	Ref	cisplatin-based chemoradiation (RADPLAT)
NCMF1363348531	3615	Squamous Cell Carcinoma	"cured, no recurrence"	oropharynx	Extract 3615	Labeled Extract 3615	Cy3	cisplatin-based chemoradiation (RADPLAT)	E-NCMF-8-raw-data-1363348531.txt	Ref	cisplatin-based chemoradiation (RADPLAT)
NCMF1363348549	3615	Squamous Cell Carcinoma	"cured, no recurrence"	oropharynx	Extract 3615	Labeled Extract 3615	Cy5	cisplatin-based chemoradiation (RADPLAT)	E-NCMF-8-raw-data-1363348549.txt	Ref	cisplatin-based chemoradiation (RADPLAT)
NCMF1363348585	3616	Squamous Cell Carcinoma	locoregional recurrence	oral cavity	Extract 3616	Labeled Extract 3616	Cy5	cisplatin-based chemoradiation (RADPLAT)	E-NCMF-8-raw-data-1363348585.txt	Ref	cisplatin-based chemoradiation (RADPLAT)
NCMF1363348603	3617	Squamous Cell Carcinoma	"cured, no recurrence"	hypopharynx	Extract 3617	Labeled Extract 3617	Cy3	cisplatin-based chemoradiation (RADPLAT)	E-NCMF-8-raw-data-1363348603.txt	Ref	cisplatin-based chemoradiation (RADPLAT)
NCMF1363348639	3617	Squamous Cell Carcinoma	"cured, no recurrence"	hypopharynx	Extract 3617	Labeled Extract 3617	Cy5	cisplatin-based chemoradiation (RADPLAT)	E-NCMF-8-raw-data-1363348639.txt	Ref	cisplatin-based chemoradiation (RADPLAT)
NCMF1363348621	3619	Squamous Cell Carcinoma	"cured, no recurrence"	oropharynx	Extract 3619	Labeled Extract 3619	Cy5	cisplatin-based chemoradiation (RADPLAT)	E-NCMF-8-raw-data-1363348621.txt	Ref	cisplatin-based chemoradiation (RADPLAT)
NCMF1363348657	3619	Squamous Cell Carcinoma	"cured, no recurrence"	oropharynx	Extract 3619	Labeled Extract 3619	Cy3	cisplatin-based chemoradiation (RADPLAT)	E-NCMF-8-raw-data-1363348657.txt	Ref	cisplatin-based chemoradiation (RADPLAT)
NCMF1363348711	3621	Squamous Cell Carcinoma	locoregional recurrence	oropharynx	Extract 3621	Labeled Extract 3621	Cy3	cisplatin-based chemoradiation (RADPLAT)	E-NCMF-8-raw-data-1363348711.txt	Ref	cisplatin-based chemoradiation (RADPLAT)
NCMF1363347343	3622	Squamous Cell Carcinoma	locoregional recurrence	oral cavity	Extract 3622	Labeled Extract 3622	Cy5	cisplatin-based chemoradiation (RADPLAT)	E-NCMF-8-raw-data-1363347343.txt	Ref	cisplatin-based chemoradiation (RADPLAT)
NCMF1363347379	3622	Squamous Cell Carcinoma	locoregional recurrence	oral cavity	Extract 3622	Labeled Extract 3622	Cy3	cisplatin-based chemoradiation (RADPLAT)	E-NCMF-8-raw-data-1363347379.txt	Ref	cisplatin-based chemoradiation (RADPLAT)
NCMF1363348369	3623	Squamous Cell Carcinoma	"cured, no recurrence"	oral cavity	Extract 3623	Labeled Extract 3623	Cy5	cisplatin-based chemoradiation (RADPLAT)	E-NCMF-8-raw-data-1363348369.txt	Ref	cisplatin-based chemoradiation (RADPLAT)
NCMF1363348405	3623	Squamous Cell Carcinoma	"cured, no recurrence"	oral cavity	Extract 3623	Labeled Extract 3623	Cy3	cisplatin-based chemoradiation (RADPLAT)	E-NCMF-8-raw-data-1363348405.txt	Ref	cisplatin-based chemoradiation (RADPLAT)
NCMF1363349359	3740	Squamous Cell Carcinoma	"cured, no recurrence"	larynx	Extract 3740	Labeled Extract 3740	Cy3	cisplatin-based chemoradiation (RADPLAT)	E-NCMF-8-raw-data-1363349359.txt	Ref	cisplatin-based chemoradiation (RADPLAT)
NCMF1363349395	3741	Squamous Cell Carcinoma	"cured, no recurrence"	larynx	Extract 3741	Labeled Extract 3741	Cy5	cisplatin-based chemoradiation (RADPLAT)	E-NCMF-8-raw-data-1363349395.txt	Ref	cisplatin-based chemoradiation (RADPLAT)
NCMF1363349431	3741	Squamous Cell Carcinoma	"cured, no recurrence"	larynx	Extract 3741	Labeled Extract 3741	Cy3	cisplatin-based chemoradiation (RADPLAT)	E-NCMF-8-raw-data-1363349431.txt	Ref	cisplatin-based chemoradiation (RADPLAT)
NCMF1363349449	3742	Squamous Cell Carcinoma	"cured, no recurrence"	oropharynx	Extract 3742	Labeled Extract 3742	Cy3	cisplatin-based chemoradiation (RADPLAT)	E-NCMF-8-raw-data-1363349449.txt	Ref	cisplatin-based chemoradiation (RADPLAT)
NCMF1363349521	3744	Squamous Cell Carcinoma	"cured, no recurrence"	oropharynx	Extract 3744	Labeled Extract 3744	Cy5	cisplatin-based chemoradiation (RADPLAT)	E-NCMF-8-raw-data-1363349521.txt	Ref	cisplatin-based chemoradiation (RADPLAT)
NCMF1363349611	3746	Squamous Cell Carcinoma	"cured, no recurrence"	oropharynx	Extract 3746	Labeled Extract 3746	Cy5	cisplatin-based chemoradiation (RADPLAT)	E-NCMF-8-raw-data-1363349611.txt	Ref	cisplatin-based chemoradiation (RADPLAT)
NCMF1363349071	3769	Squamous Cell Carcinoma	"cured, no recurrence"	larynx	Extract 3769	Labeled Extract 3769	Cy3	cisplatin-based chemoradiation (RADPLAT)	E-NCMF-8-raw-data-1363349071.txt	Ref	cisplatin-based chemoradiation (RADPLAT)
NCMF1363349089	3769	Squamous Cell Carcinoma	"cured, no recurrence"	larynx	Extract 3769	Labeled Extract 3769	Cy5	cisplatin-based chemoradiation (RADPLAT)	E-NCMF-8-raw-data-1363349089.txt	Ref	cisplatin-based chemoradiation (RADPLAT)
NCMF1363349197	3772	Squamous Cell Carcinoma	"cured, no recurrence"	oropharynx	Extract 3772	Labeled Extract 3772	Cy5	cisplatin-based chemoradiation (RADPLAT)	E-NCMF-8-raw-data-1363349197.txt	Ref	cisplatin-based chemoradiation (RADPLAT)
NCMF1363349233	3773	Squamous Cell Carcinoma	locoregional recurrence	oropharynx	Extract 3773	Labeled Extract 3773	Cy5	cisplatin-based chemoradiation (RADPLAT)	E-NCMF-8-raw-data-1363349233.txt	Ref	cisplatin-based chemoradiation (RADPLAT)
NCMF1363348963	3775	Squamous Cell Carcinoma	"cured, no recurrence"	oropharynx	Extract 3775	Labeled Extract 3775	Cy5	cisplatin-based chemoradiation (RADPLAT)	E-NCMF-8-raw-data-1363348963.txt	Ref	cisplatin-based chemoradiation (RADPLAT)
NCMF1363348981	3775	Squamous Cell Carcinoma	"cured, no recurrence"	oropharynx	Extract 3775	Labeled Extract 3775	Cy3	cisplatin-based chemoradiation (RADPLAT)	E-NCMF-8-raw-data-1363348981.txt	Ref	cisplatin-based chemoradiation (RADPLAT)
NCMF1363349035	3776	Squamous Cell Carcinoma	"cured, no recurrence"	larynx	Extract 3776	Labeled Extract 3776	Cy5	cisplatin-based chemoradiation (RADPLAT)	E-NCMF-8-raw-data-1363349035.txt	Ref	cisplatin-based chemoradiation (RADPLAT)
NCMF1363349791	3778	Squamous Cell Carcinoma	locoregional recurrence	oral cavity	Extract 3778	Labeled Extract 3778	Cy3	cisplatin-based chemoradiation (RADPLAT)	E-NCMF-8-raw-data-1363349791.txt	Ref	cisplatin-based chemoradiation (RADPLAT)
NCMF1363349971	3782	Squamous Cell Carcinoma	"cured, no recurrence"	oropharynx	Extract 3782	Labeled Extract 3782	Cy3	cisplatin-based chemoradiation (RADPLAT)	E-NCMF-8-raw-data-1363349971.txt	Ref	cisplatin-based chemoradiation (RADPLAT)
NCMF1363350007	3782	Squamous Cell Carcinoma	"cured, no recurrence"	oropharynx	Extract 3782	Labeled Extract 3782	Cy5	cisplatin-based chemoradiation (RADPLAT)	E-NCMF-8-raw-data-1363350007.txt	Ref	cisplatin-based chemoradiation (RADPLAT)
NCMF1363350043	3783	Squamous Cell Carcinoma	locoregional recurrence	oral cavity	Extract 3783	Labeled Extract 3783	Cy5	cisplatin-based chemoradiation (RADPLAT)	E-NCMF-8-raw-data-1363350043.txt	Ref	cisplatin-based chemoradiation (RADPLAT)
NCMF1363350097	3786	Squamous Cell Carcinoma	"cured, no recurrence"	larynx	Extract 3786	Labeled Extract 3786	Cy5	cisplatin-based chemoradiation (RADPLAT)	E-NCMF-8-raw-data-1363350097.txt	Ref	cisplatin-based chemoradiation (RADPLAT)
NCMF1363349143	3787	Squamous Cell Carcinoma	"cured, no recurrence"	oropharynx	Extract 3787	Labeled Extract 3787	Cy5	cisplatin-based chemoradiation (RADPLAT)	E-NCMF-8-raw-data-1363349143.txt	Ref	cisplatin-based chemoradiation (RADPLAT)
NCMF1363349179	3787	Squamous Cell Carcinoma	"cured, no recurrence"	oropharynx	Extract 3787	Labeled Extract 3787	Cy3	cisplatin-based chemoradiation (RADPLAT)	E-NCMF-8-raw-data-1363349179.txt	Ref	cisplatin-based chemoradiation (RADPLAT)
NCMF1363349881	11A	Squamous Cell Carcinoma		oral cavity	Extract 11A	Labeled Extract 11A	Cy5	untreated	E-NCMF-8-raw-data-1363349881.txt	Ref	untreated
NCMF1363349845	11B	Squamous Cell Carcinoma		oral cavity	Extract 11B	Labeled Extract 11B	Cy5	untreated	E-NCMF-8-raw-data-1363349845.txt	Ref	untreated
NCMF1363349917	11B	Squamous Cell Carcinoma		oral cavity	Extract 11B	Labeled Extract 11B	Cy3	untreated	E-NCMF-8-raw-data-1363349917.txt	Ref	untreated
NCMF1363350133	12A	Squamous Cell Carcinoma		oral cavity	Extract 12A	Labeled Extract 12A	Cy3	untreated	E-NCMF-8-raw-data-1363350133.txt	Ref	untreated
NCMF1363350169	12B	Squamous Cell Carcinoma		oral cavity	Extract 12B	Labeled Extract 12B	Cy5	untreated	E-NCMF-8-raw-data-1363350169.txt	Ref	untreated
NCMF1363350187	13A	Squamous Cell Carcinoma		oropharynx	Extract 13A	Labeled Extract 13A	Cy5	untreated	E-NCMF-8-raw-data-1363350187.txt	Ref	untreated
NCMF1363350205	13A	Squamous Cell Carcinoma		oropharynx	Extract 13A	Labeled Extract 13A	Cy3	untreated	E-NCMF-8-raw-data-1363350205.txt	Ref	untreated
NCMF1363350223	13B	Squamous Cell Carcinoma		oropharynx	Extract 13B	Labeled Extract 13B	Cy3	untreated	E-NCMF-8-raw-data-1363350223.txt	Ref	untreated
NCMF1363349899	common head and neck reference pool of 61 HNSCC	Squamous Cell Carcinoma			Extract common head and neck reference pool of 61 HNSCC	Labeled Extract common head and neck reference pool of 61 HNSCC	Cy5	untreated	E-NCMF-8-raw-data-1363349899.txt	Ref	untreated
NCMF1363350115	common head and neck reference pool of 61 HNSCC	Squamous Cell Carcinoma			Extract common head and neck reference pool of 61 HNSCC	Labeled Extract common head and neck reference pool of 61 HNSCC	Cy5	untreated	E-NCMF-8-raw-data-1363350115.txt	Ref	untreated
NCMF1363350151	common head and neck reference pool of 61 HNSCC	Squamous Cell Carcinoma			Extract common head and neck reference pool of 61 HNSCC	Labeled Extract common head and neck reference pool of 61 HNSCC	Cy3	untreated	E-NCMF-8-raw-data-1363350151.txt	Ref	untreated
NCMF1363350241	common head and neck reference pool of 61 HNSCC	Squamous Cell Carcinoma			Extract common head and neck reference pool of 61 HNSCC	Labeled Extract common head and neck reference pool of 61 HNSCC	Cy3	untreated	E-NCMF-8-raw-data-1363350241.txt	Ref	untreated
NCMF1363346856	reference pool of 61 HNSCC	Squamous Cell Carcinoma			Extract reference pool of 61 HNSCC	Labeled Extract reference pool of 61 HNSCC	Cy5	cisplatin-based chemoradiation (RADPLAT)	E-NCMF-8-raw-data-1363346856.txt	Ref	cisplatin-based chemoradiation (RADPLAT)
NCMF1363346874	reference pool of 61 HNSCC	Squamous Cell Carcinoma			Extract reference pool of 61 HNSCC	Labeled Extract reference pool of 61 HNSCC	Cy3	cisplatin-based chemoradiation (RADPLAT)	E-NCMF-8-raw-data-1363346874.txt	Ref	cisplatin-based chemoradiation (RADPLAT)
NCMF1363346910	reference pool of 61 HNSCC	Squamous Cell Carcinoma			Extract reference pool of 61 HNSCC	Labeled Extract reference pool of 61 HNSCC	Cy5	cisplatin-based chemoradiation (RADPLAT)	E-NCMF-8-raw-data-1363346910.txt	Ref	cisplatin-based chemoradiation (RADPLAT)
NCMF1363346946	reference pool of 61 HNSCC	Squamous Cell Carcinoma			Extract reference pool of 61 HNSCC	Labeled Extract reference pool of 61 HNSCC	Cy3	cisplatin-based chemoradiation (RADPLAT)	E-NCMF-8-raw-data-1363346946.txt	Ref	cisplatin-based chemoradiation (RADPLAT)
NCMF1363346964	reference pool of 61 HNSCC	Squamous Cell Carcinoma			Extract reference pool of 61 HNSCC	Labeled Extract reference pool of 61 HNSCC	Cy3	cisplatin-based chemoradiation (RADPLAT)	E-NCMF-8-raw-data-1363346964.txt	Ref	cisplatin-based chemoradiation (RADPLAT)
NCMF1363347000	reference pool of 61 HNSCC	Squamous Cell Carcinoma			Extract reference pool of 61 HNSCC	Labeled Extract reference pool of 61 HNSCC	Cy3	cisplatin-based chemoradiation (RADPLAT)	E-NCMF-8-raw-data-1363347000.txt	Ref	cisplatin-based chemoradiation (RADPLAT)
NCMF1363347018	reference pool of 61 HNSCC	Squamous Cell Carcinoma			Extract reference pool of 61 HNSCC	Labeled Extract reference pool of 61 HNSCC	Cy5	cisplatin-based chemoradiation (RADPLAT)	E-NCMF-8-raw-data-1363347018.txt	Ref	cisplatin-based chemoradiation (RADPLAT)
NCMF1363347072	reference pool of 61 HNSCC	Squamous Cell Carcinoma			Extract reference pool of 61 HNSCC	Labeled Extract reference pool of 61 HNSCC	Cy3	cisplatin-based chemoradiation (RADPLAT)	E-NCMF-8-raw-data-1363347072.txt	Ref	cisplatin-based chemoradiation (RADPLAT)
NCMF1363347162	reference pool of 61 HNSCC	Squamous Cell Carcinoma			Extract reference pool of 61 HNSCC	Labeled Extract reference pool of 61 HNSCC	Cy5	cisplatin-based chemoradiation (RADPLAT)	E-NCMF-8-raw-data-1363347162.txt	Ref	cisplatin-based chemoradiation (RADPLAT)
NCMF1363347180	reference pool of 61 HNSCC	Squamous Cell Carcinoma			Extract reference pool of 61 HNSCC	Labeled Extract reference pool of 61 HNSCC	Cy3	cisplatin-based chemoradiation (RADPLAT)	E-NCMF-8-raw-data-1363347180.txt	Ref	cisplatin-based chemoradiation (RADPLAT)
NCMF1363347216	reference pool of 61 HNSCC	Squamous Cell Carcinoma			Extract reference pool of 61 HNSCC	Labeled Extract reference pool of 61 HNSCC	Cy5	cisplatin-based chemoradiation (RADPLAT)	E-NCMF-8-raw-data-1363347216.txt	Ref	cisplatin-based chemoradiation (RADPLAT)
NCMF1363347234	reference pool of 61 HNSCC	Squamous Cell Carcinoma			Extract reference pool of 61 HNSCC	Labeled Extract reference pool of 61 HNSCC	Cy3	cisplatin-based chemoradiation (RADPLAT)	E-NCMF-8-raw-data-1363347234.txt	Ref	cisplatin-based chemoradiation (RADPLAT)
NCMF1363347271	reference pool of 61 HNSCC	Squamous Cell Carcinoma			Extract reference pool of 61 HNSCC	Labeled Extract reference pool of 61 HNSCC	Cy3	cisplatin-based chemoradiation (RADPLAT)	E-NCMF-8-raw-data-1363347271.txt	Ref	cisplatin-based chemoradiation (RADPLAT)
NCMF1363347325	reference pool of 61 HNSCC	Squamous Cell Carcinoma			Extract reference pool of 61 HNSCC	Labeled Extract reference pool of 61 HNSCC	Cy3	cisplatin-based chemoradiation (RADPLAT)	E-NCMF-8-raw-data-1363347325.txt	Ref	cisplatin-based chemoradiation (RADPLAT)
NCMF1363347433	reference pool of 61 HNSCC	Squamous Cell Carcinoma			Extract reference pool of 61 HNSCC	Labeled Extract reference pool of 61 HNSCC	Cy3	cisplatin-based chemoradiation (RADPLAT)	E-NCMF-8-raw-data-1363347433.txt	Ref	cisplatin-based chemoradiation (RADPLAT)
NCMF1363347487	reference pool of 61 HNSCC	Squamous Cell Carcinoma			Extract reference pool of 61 HNSCC	Labeled Extract reference pool of 61 HNSCC	Cy5	cisplatin-based chemoradiation (RADPLAT)	E-NCMF-8-raw-data-1363347487.txt	Ref	cisplatin-based chemoradiation (RADPLAT)
NCMF1363347541	reference pool of 61 HNSCC	Squamous Cell Carcinoma			Extract reference pool of 61 HNSCC	Labeled Extract reference pool of 61 HNSCC	Cy3	cisplatin-based chemoradiation (RADPLAT)	E-NCMF-8-raw-data-1363347541.txt	Ref	cisplatin-based chemoradiation (RADPLAT)
NCMF1363347577	reference pool of 61 HNSCC	Squamous Cell Carcinoma			Extract reference pool of 61 HNSCC	Labeled Extract reference pool of 61 HNSCC	Cy5	cisplatin-based chemoradiation (RADPLAT)	E-NCMF-8-raw-data-1363347577.txt	Ref	cisplatin-based chemoradiation (RADPLAT)
NCMF1363347703	reference pool of 61 HNSCC	Squamous Cell Carcinoma			Extract reference pool of 61 HNSCC	Labeled Extract reference pool of 61 HNSCC	Cy5	cisplatin-based chemoradiation (RADPLAT)	E-NCMF-8-raw-data-1363347703.txt	Ref	cisplatin-based chemoradiation (RADPLAT)
NCMF1363347739	reference pool of 61 HNSCC	Squamous Cell Carcinoma			Extract reference pool of 61 HNSCC	Labeled Extract reference pool of 61 HNSCC	Cy5	cisplatin-based chemoradiation (RADPLAT)	E-NCMF-8-raw-data-1363347739.txt	Ref	cisplatin-based chemoradiation (RADPLAT)
NCMF1363347757	reference pool of 61 HNSCC	Squamous Cell Carcinoma			Extract reference pool of 61 HNSCC	Labeled Extract reference pool of 61 HNSCC	Cy3	cisplatin-based chemoradiation (RADPLAT)	E-NCMF-8-raw-data-1363347757.txt	Ref	cisplatin-based chemoradiation (RADPLAT)
NCMF1363347793	reference pool of 61 HNSCC	Squamous Cell Carcinoma			Extract reference pool of 61 HNSCC	Labeled Extract reference pool of 61 HNSCC	Cy5	cisplatin-based chemoradiation (RADPLAT)	E-NCMF-8-raw-data-1363347793.txt	Ref	cisplatin-based chemoradiation (RADPLAT)
NCMF1363347811	reference pool of 61 HNSCC	Squamous Cell Carcinoma			Extract reference pool of 61 HNSCC	Labeled Extract reference pool of 61 HNSCC	Cy3	cisplatin-based chemoradiation (RADPLAT)	E-NCMF-8-raw-data-1363347811.txt	Ref	cisplatin-based chemoradiation (RADPLAT)
NCMF1363347865	reference pool of 61 HNSCC	Squamous Cell Carcinoma			Extract reference pool of 61 HNSCC	Labeled Extract reference pool of 61 HNSCC	Cy3	cisplatin-based chemoradiation (RADPLAT)	E-NCMF-8-raw-data-1363347865.txt	Ref	cisplatin-based chemoradiation (RADPLAT)
NCMF1363347901	reference pool of 61 HNSCC	Squamous Cell Carcinoma			Extract reference pool of 61 HNSCC	Labeled Extract reference pool of 61 HNSCC	Cy3	cisplatin-based chemoradiation (RADPLAT)	E-NCMF-8-raw-data-1363347901.txt	Ref	cisplatin-based chemoradiation (RADPLAT)
NCMF1363347919	reference pool of 61 HNSCC	Squamous Cell Carcinoma			Extract reference pool of 61 HNSCC	Labeled Extract reference pool of 61 HNSCC	Cy5	cisplatin-based chemoradiation (RADPLAT)	E-NCMF-8-raw-data-1363347919.txt	Ref	cisplatin-based chemoradiation (RADPLAT)
NCMF1363347955	reference pool of 61 HNSCC	Squamous Cell Carcinoma			Extract reference pool of 61 HNSCC	Labeled Extract reference pool of 61 HNSCC	Cy3	cisplatin-based chemoradiation (RADPLAT)	E-NCMF-8-raw-data-1363347955.txt	Ref	cisplatin-based chemoradiation (RADPLAT)
NCMF1363347973	reference pool of 61 HNSCC	Squamous Cell Carcinoma			Extract reference pool of 61 HNSCC	Labeled Extract reference pool of 61 HNSCC	Cy3	cisplatin-based chemoradiation (RADPLAT)	E-NCMF-8-raw-data-1363347973.txt	Ref	cisplatin-based chemoradiation (RADPLAT)
NCMF1363348081	reference pool of 61 HNSCC	Squamous Cell Carcinoma			Extract reference pool of 61 HNSCC	Labeled Extract reference pool of 61 HNSCC	Cy3	cisplatin-based chemoradiation (RADPLAT)	E-NCMF-8-raw-data-1363348081.txt	Ref	cisplatin-based chemoradiation (RADPLAT)
NCMF1363348099	reference pool of 61 HNSCC	Squamous Cell Carcinoma			Extract reference pool of 61 HNSCC	Labeled Extract reference pool of 61 HNSCC	Cy5	cisplatin-based chemoradiation (RADPLAT)	E-NCMF-8-raw-data-1363348099.txt	Ref	cisplatin-based chemoradiation (RADPLAT)
NCMF1363348135	reference pool of 61 HNSCC	Squamous Cell Carcinoma			Extract reference pool of 61 HNSCC	Labeled Extract reference pool of 61 HNSCC	Cy5	cisplatin-based chemoradiation (RADPLAT)	E-NCMF-8-raw-data-1363348135.txt	Ref	cisplatin-based chemoradiation (RADPLAT)
NCMF1363348153	reference pool of 61 HNSCC	Squamous Cell Carcinoma			Extract reference pool of 61 HNSCC	Labeled Extract reference pool of 61 HNSCC	Cy3	cisplatin-based chemoradiation (RADPLAT)	E-NCMF-8-raw-data-1363348153.txt	Ref	cisplatin-based chemoradiation (RADPLAT)
NCMF1363348171	reference pool of 61 HNSCC	Squamous Cell Carcinoma			Extract reference pool of 61 HNSCC	Labeled Extract reference pool of 61 HNSCC	Cy3	cisplatin-based chemoradiation (RADPLAT)	E-NCMF-8-raw-data-1363348171.txt	Ref	cisplatin-based chemoradiation (RADPLAT)
NCMF1363348189	reference pool of 61 HNSCC	Squamous Cell Carcinoma			Extract reference pool of 61 HNSCC	Labeled Extract reference pool of 61 HNSCC	Cy5	cisplatin-based chemoradiation (RADPLAT)	E-NCMF-8-raw-data-1363348189.txt	Ref	cisplatin-based chemoradiation (RADPLAT)
NCMF1363348261	reference pool of 61 HNSCC	Squamous Cell Carcinoma			Extract reference pool of 61 HNSCC	Labeled Extract reference pool of 61 HNSCC	Cy5	cisplatin-based chemoradiation (RADPLAT)	E-NCMF-8-raw-data-1363348261.txt	Ref	cisplatin-based chemoradiation (RADPLAT)
NCMF1363348297	reference pool of 61 HNSCC	Squamous Cell Carcinoma			Extract reference pool of 61 HNSCC	Labeled Extract reference pool of 61 HNSCC	Cy3	cisplatin-based chemoradiation (RADPLAT)	E-NCMF-8-raw-data-1363348297.txt	Ref	cisplatin-based chemoradiation (RADPLAT)
NCMF1363348315	reference pool of 61 HNSCC	Squamous Cell Carcinoma			Extract reference pool of 61 HNSCC	Labeled Extract reference pool of 61 HNSCC	Cy3	cisplatin-based chemoradiation (RADPLAT)	E-NCMF-8-raw-data-1363348315.txt	Ref	cisplatin-based chemoradiation (RADPLAT)
NCMF1363348351	reference pool of 61 HNSCC	Squamous Cell Carcinoma			Extract reference pool of 61 HNSCC	Labeled Extract reference pool of 61 HNSCC	Cy5	cisplatin-based chemoradiation (RADPLAT)	E-NCMF-8-raw-data-1363348351.txt	Ref	cisplatin-based chemoradiation (RADPLAT)
NCMF1363348387	reference pool of 61 HNSCC	Squamous Cell Carcinoma			Extract reference pool of 61 HNSCC	Labeled Extract reference pool of 61 HNSCC	Cy3	cisplatin-based chemoradiation (RADPLAT)	E-NCMF-8-raw-data-1363348387.txt	Ref	cisplatin-based chemoradiation (RADPLAT)
NCMF1363348441	reference pool of 61 HNSCC	Squamous Cell Carcinoma			Extract reference pool of 61 HNSCC	Labeled Extract reference pool of 61 HNSCC	Cy5	cisplatin-based chemoradiation (RADPLAT)	E-NCMF-8-raw-data-1363348441.txt	Ref	cisplatin-based chemoradiation (RADPLAT)
NCMF1363348459	reference pool of 61 HNSCC	Squamous Cell Carcinoma			Extract reference pool of 61 HNSCC	Labeled Extract reference pool of 61 HNSCC	Cy5	cisplatin-based chemoradiation (RADPLAT)	E-NCMF-8-raw-data-1363348459.txt	Ref	cisplatin-based chemoradiation (RADPLAT)
NCMF1363348477	reference pool of 61 HNSCC	Squamous Cell Carcinoma			Extract reference pool of 61 HNSCC	Labeled Extract reference pool of 61 HNSCC	Cy3	cisplatin-based chemoradiation (RADPLAT)	E-NCMF-8-raw-data-1363348477.txt	Ref	cisplatin-based chemoradiation (RADPLAT)
NCMF1363348513	reference pool of 61 HNSCC	Squamous Cell Carcinoma			Extract reference pool of 61 HNSCC	Labeled Extract reference pool of 61 HNSCC	Cy5	cisplatin-based chemoradiation (RADPLAT)	E-NCMF-8-raw-data-1363348513.txt	Ref	cisplatin-based chemoradiation (RADPLAT)
NCMF1363348567	reference pool of 61 HNSCC	Squamous Cell Carcinoma			Extract reference pool of 61 HNSCC	Labeled Extract reference pool of 61 HNSCC	Cy5	cisplatin-based chemoradiation (RADPLAT)	E-NCMF-8-raw-data-1363348567.txt	Ref	cisplatin-based chemoradiation (RADPLAT)
NCMF1363348675	reference pool of 61 HNSCC	Squamous Cell Carcinoma			Extract reference pool of 61 HNSCC	Labeled Extract reference pool of 61 HNSCC	Cy5	cisplatin-based chemoradiation (RADPLAT)	E-NCMF-8-raw-data-1363348675.txt	Ref	cisplatin-based chemoradiation (RADPLAT)
NCMF1363348693	reference pool of 61 HNSCC	Squamous Cell Carcinoma			Extract reference pool of 61 HNSCC	Labeled Extract reference pool of 61 HNSCC	Cy3	cisplatin-based chemoradiation (RADPLAT)	E-NCMF-8-raw-data-1363348693.txt	Ref	cisplatin-based chemoradiation (RADPLAT)
NCMF1363348729	reference pool of 61 HNSCC	Squamous Cell Carcinoma			Extract reference pool of 61 HNSCC	Labeled Extract reference pool of 61 HNSCC	Cy3	cisplatin-based chemoradiation (RADPLAT)	E-NCMF-8-raw-data-1363348729.txt	Ref	cisplatin-based chemoradiation (RADPLAT)
NCMF1363348747	reference pool of 61 HNSCC	Squamous Cell Carcinoma			Extract reference pool of 61 HNSCC	Labeled Extract reference pool of 61 HNSCC	Cy5	cisplatin-based chemoradiation (RADPLAT)	E-NCMF-8-raw-data-1363348747.txt	Ref	cisplatin-based chemoradiation (RADPLAT)
NCMF1363348783	reference pool of 61 HNSCC	Squamous Cell Carcinoma			Extract reference pool of 61 HNSCC	Labeled Extract reference pool of 61 HNSCC	Cy5	cisplatin-based chemoradiation (RADPLAT)	E-NCMF-8-raw-data-1363348783.txt	Ref	cisplatin-based chemoradiation (RADPLAT)
NCMF1363348837	reference pool of 61 HNSCC	Squamous Cell Carcinoma			Extract reference pool of 61 HNSCC	Labeled Extract reference pool of 61 HNSCC	Cy3	cisplatin-based chemoradiation (RADPLAT)	E-NCMF-8-raw-data-1363348837.txt	Ref	cisplatin-based chemoradiation (RADPLAT)
NCMF1363348891	reference pool of 61 HNSCC	Squamous Cell Carcinoma			Extract reference pool of 61 HNSCC	Labeled Extract reference pool of 61 HNSCC	Cy5	cisplatin-based chemoradiation (RADPLAT)	E-NCMF-8-raw-data-1363348891.txt	Ref	cisplatin-based chemoradiation (RADPLAT)
NCMF1363348909	reference pool of 61 HNSCC	Squamous Cell Carcinoma			Extract reference pool of 61 HNSCC	Labeled Extract reference pool of 61 HNSCC	Cy3	cisplatin-based chemoradiation (RADPLAT)	E-NCMF-8-raw-data-1363348909.txt	Ref	cisplatin-based chemoradiation (RADPLAT)
NCMF1363348927	reference pool of 61 HNSCC	Squamous Cell Carcinoma			Extract reference pool of 61 HNSCC	Labeled Extract reference pool of 61 HNSCC	Cy3	cisplatin-based chemoradiation (RADPLAT)	E-NCMF-8-raw-data-1363348927.txt	Ref	cisplatin-based chemoradiation (RADPLAT)
NCMF1363348945	reference pool of 61 HNSCC	Squamous Cell Carcinoma			Extract reference pool of 61 HNSCC	Labeled Extract reference pool of 61 HNSCC	Cy5	cisplatin-based chemoradiation (RADPLAT)	E-NCMF-8-raw-data-1363348945.txt	Ref	cisplatin-based chemoradiation (RADPLAT)
NCMF1363348999	reference pool of 61 HNSCC	Squamous Cell Carcinoma			Extract reference pool of 61 HNSCC	Labeled Extract reference pool of 61 HNSCC	Cy5	cisplatin-based chemoradiation (RADPLAT)	E-NCMF-8-raw-data-1363348999.txt	Ref	cisplatin-based chemoradiation (RADPLAT)
NCMF1363349017	reference pool of 61 HNSCC	Squamous Cell Carcinoma			Extract reference pool of 61 HNSCC	Labeled Extract reference pool of 61 HNSCC	Cy5	cisplatin-based chemoradiation (RADPLAT)	E-NCMF-8-raw-data-1363349017.txt	Ref	cisplatin-based chemoradiation (RADPLAT)
NCMF1363349053	reference pool of 61 HNSCC	Squamous Cell Carcinoma			Extract reference pool of 61 HNSCC	Labeled Extract reference pool of 61 HNSCC	Cy3	cisplatin-based chemoradiation (RADPLAT)	E-NCMF-8-raw-data-1363349053.txt	Ref	cisplatin-based chemoradiation (RADPLAT)
NCMF1363349107	reference pool of 61 HNSCC	Squamous Cell Carcinoma			Extract reference pool of 61 HNSCC	Labeled Extract reference pool of 61 HNSCC	Cy3	cisplatin-based chemoradiation (RADPLAT)	E-NCMF-8-raw-data-1363349107.txt	Ref	cisplatin-based chemoradiation (RADPLAT)
NCMF1363349125	reference pool of 61 HNSCC	Squamous Cell Carcinoma			Extract reference pool of 61 HNSCC	Labeled Extract reference pool of 61 HNSCC	Cy5	cisplatin-based chemoradiation (RADPLAT)	E-NCMF-8-raw-data-1363349125.txt	Ref	cisplatin-based chemoradiation (RADPLAT)
NCMF1363349161	reference pool of 61 HNSCC	Squamous Cell Carcinoma			Extract reference pool of 61 HNSCC	Labeled Extract reference pool of 61 HNSCC	Cy5	cisplatin-based chemoradiation (RADPLAT)	E-NCMF-8-raw-data-1363349161.txt	Ref	cisplatin-based chemoradiation (RADPLAT)
NCMF1363349215	reference pool of 61 HNSCC	Squamous Cell Carcinoma			Extract reference pool of 61 HNSCC	Labeled Extract reference pool of 61 HNSCC	Cy5	cisplatin-based chemoradiation (RADPLAT)	E-NCMF-8-raw-data-1363349215.txt	Ref	cisplatin-based chemoradiation (RADPLAT)
NCMF1363349287	reference pool of 61 HNSCC	Squamous Cell Carcinoma			Extract reference pool of 61 HNSCC	Labeled Extract reference pool of 61 HNSCC	Cy5	cisplatin-based chemoradiation (RADPLAT)	E-NCMF-8-raw-data-1363349287.txt	Ref	cisplatin-based chemoradiation (RADPLAT)
NCMF1363349305	reference pool of 61 HNSCC	Squamous Cell Carcinoma			Extract reference pool of 61 HNSCC	Labeled Extract reference pool of 61 HNSCC	Cy3	cisplatin-based chemoradiation (RADPLAT)	E-NCMF-8-raw-data-1363349305.txt	Ref	cisplatin-based chemoradiation (RADPLAT)
NCMF1363349323	reference pool of 61 HNSCC	Squamous Cell Carcinoma			Extract reference pool of 61 HNSCC	Labeled Extract reference pool of 61 HNSCC	Cy3	cisplatin-based chemoradiation (RADPLAT)	E-NCMF-8-raw-data-1363349323.txt	Ref	cisplatin-based chemoradiation (RADPLAT)
NCMF1363349341	reference pool of 61 HNSCC	Squamous Cell Carcinoma			Extract reference pool of 61 HNSCC	Labeled Extract reference pool of 61 HNSCC	Cy5	cisplatin-based chemoradiation (RADPLAT)	E-NCMF-8-raw-data-1363349341.txt	Ref	cisplatin-based chemoradiation (RADPLAT)
NCMF1363349377	reference pool of 61 HNSCC	Squamous Cell Carcinoma			Extract reference pool of 61 HNSCC	Labeled Extract reference pool of 61 HNSCC	Cy3	cisplatin-based chemoradiation (RADPLAT)	E-NCMF-8-raw-data-1363349377.txt	Ref	cisplatin-based chemoradiation (RADPLAT)
NCMF1363349413	reference pool of 61 HNSCC	Squamous Cell Carcinoma			Extract reference pool of 61 HNSCC	Labeled Extract reference pool of 61 HNSCC	Cy3	cisplatin-based chemoradiation (RADPLAT)	E-NCMF-8-raw-data-1363349413.txt	Ref	cisplatin-based chemoradiation (RADPLAT)
NCMF1363349467	reference pool of 61 HNSCC	Squamous Cell Carcinoma			Extract reference pool of 61 HNSCC	Labeled Extract reference pool of 61 HNSCC	Cy5	cisplatin-based chemoradiation (RADPLAT)	E-NCMF-8-raw-data-1363349467.txt	Ref	cisplatin-based chemoradiation (RADPLAT)
NCMF1363349485	reference pool of 61 HNSCC	Squamous Cell Carcinoma			Extract reference pool of 61 HNSCC	Labeled Extract reference pool of 61 HNSCC	Cy3	cisplatin-based chemoradiation (RADPLAT)	E-NCMF-8-raw-data-1363349485.txt	Ref	cisplatin-based chemoradiation (RADPLAT)
NCMF1363349503	reference pool of 61 HNSCC	Squamous Cell Carcinoma			Extract reference pool of 61 HNSCC	Labeled Extract reference pool of 61 HNSCC	Cy5	cisplatin-based chemoradiation (RADPLAT)	E-NCMF-8-raw-data-1363349503.txt	Ref	cisplatin-based chemoradiation (RADPLAT)
NCMF1363349539	reference pool of 61 HNSCC	Squamous Cell Carcinoma			Extract reference pool of 61 HNSCC	Labeled Extract reference pool of 61 HNSCC	Cy5	cisplatin-based chemoradiation (RADPLAT)	E-NCMF-8-raw-data-1363349539.txt	Ref	cisplatin-based chemoradiation (RADPLAT)
NCMF1363349557	reference pool of 61 HNSCC	Squamous Cell Carcinoma			Extract reference pool of 61 HNSCC	Labeled Extract reference pool of 61 HNSCC	Cy5	cisplatin-based chemoradiation (RADPLAT)	E-NCMF-8-raw-data-1363349557.txt	Ref	cisplatin-based chemoradiation (RADPLAT)
NCMF1363349593	reference pool of 61 HNSCC	Squamous Cell Carcinoma			Extract reference pool of 61 HNSCC	Labeled Extract reference pool of 61 HNSCC	Cy3	cisplatin-based chemoradiation (RADPLAT)	E-NCMF-8-raw-data-1363349593.txt	Ref	cisplatin-based chemoradiation (RADPLAT)
NCMF1363349665	reference pool of 61 HNSCC	Squamous Cell Carcinoma			Extract reference pool of 61 HNSCC	Labeled Extract reference pool of 61 HNSCC	Cy3	cisplatin-based chemoradiation (RADPLAT)	E-NCMF-8-raw-data-1363349665.txt	Ref	cisplatin-based chemoradiation (RADPLAT)
NCMF1363349701	reference pool of 61 HNSCC	Squamous Cell Carcinoma			Extract reference pool of 61 HNSCC	Labeled Extract reference pool of 61 HNSCC	Cy5	cisplatin-based chemoradiation (RADPLAT)	E-NCMF-8-raw-data-1363349701.txt	Ref	cisplatin-based chemoradiation (RADPLAT)
NCMF1363349719	reference pool of 61 HNSCC	Squamous Cell Carcinoma			Extract reference pool of 61 HNSCC	Labeled Extract reference pool of 61 HNSCC	Cy3	cisplatin-based chemoradiation (RADPLAT)	E-NCMF-8-raw-data-1363349719.txt	Ref	cisplatin-based chemoradiation (RADPLAT)
NCMF1363349755	reference pool of 61 HNSCC	Squamous Cell Carcinoma			Extract reference pool of 61 HNSCC	Labeled Extract reference pool of 61 HNSCC	Cy3	cisplatin-based chemoradiation (RADPLAT)	E-NCMF-8-raw-data-1363349755.txt	Ref	cisplatin-based chemoradiation (RADPLAT)
NCMF1363349773	reference pool of 61 HNSCC	Squamous Cell Carcinoma			Extract reference pool of 61 HNSCC	Labeled Extract reference pool of 61 HNSCC	Cy5	cisplatin-based chemoradiation (RADPLAT)	E-NCMF-8-raw-data-1363349773.txt	Ref	cisplatin-based chemoradiation (RADPLAT)
NCMF1363349809	reference pool of 61 HNSCC	Squamous Cell Carcinoma			Extract reference pool of 61 HNSCC	Labeled Extract reference pool of 61 HNSCC	Cy3	cisplatin-based chemoradiation (RADPLAT)	E-NCMF-8-raw-data-1363349809.txt	Ref	cisplatin-based chemoradiation (RADPLAT)
NCMF1363349935	reference pool of 61 HNSCC	Squamous Cell Carcinoma			Extract reference pool of 61 HNSCC	Labeled Extract reference pool of 61 HNSCC	Cy3	cisplatin-based chemoradiation (RADPLAT)	E-NCMF-8-raw-data-1363349935.txt	Ref	cisplatin-based chemoradiation (RADPLAT)
NCMF1363349953	reference pool of 61 HNSCC	Squamous Cell Carcinoma			Extract reference pool of 61 HNSCC	Labeled Extract reference pool of 61 HNSCC	Cy5	cisplatin-based chemoradiation (RADPLAT)	E-NCMF-8-raw-data-1363349953.txt	Ref	cisplatin-based chemoradiation (RADPLAT)
NCMF1363349989	reference pool of 61 HNSCC	Squamous Cell Carcinoma			Extract reference pool of 61 HNSCC	Labeled Extract reference pool of 61 HNSCC	Cy5	cisplatin-based chemoradiation (RADPLAT)	E-NCMF-8-raw-data-1363349989.txt	Ref	cisplatin-based chemoradiation (RADPLAT)
NCMF1363350025	reference pool of 61 HNSCC	Squamous Cell Carcinoma			Extract reference pool of 61 HNSCC	Labeled Extract reference pool of 61 HNSCC	Cy5	cisplatin-based chemoradiation (RADPLAT)	E-NCMF-8-raw-data-1363350025.txt	Ref	cisplatin-based chemoradiation (RADPLAT)
NCMF1363350061	reference pool of 61 HNSCC	Squamous Cell Carcinoma			Extract reference pool of 61 HNSCC	Labeled Extract reference pool of 61 HNSCC	Cy3	cisplatin-based chemoradiation (RADPLAT)	E-NCMF-8-raw-data-1363350061.txt	Ref	cisplatin-based chemoradiation (RADPLAT)
NCMF1363350079	reference pool of 61 HNSCC	Squamous Cell Carcinoma			Extract reference pool of 61 HNSCC	Labeled Extract reference pool of 61 HNSCC	Cy5	cisplatin-based chemoradiation (RADPLAT)	E-NCMF-8-raw-data-1363350079.txt	Ref	cisplatin-based chemoradiation (RADPLAT)


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