[BioC] beadarray - combining swath files
Darren Plant
Darren.Plant at manchester.ac.uk
Thu Jun 6 14:50:49 CEST 2013
Dear Mark,
I'm running commands from my base directory
basedir<-"D:/work/RAMS"
setwd(basedir)
my sampleSheet and array data are in D:/work/RAMS/data/9259561003
I've also tried this with no luck.
> sampleSheetFile <- paste("data/9259561003", "/sampleSheet.csv", sep = "")
> readLines(sampleSheetFile)
[1] "[Header],,," "Investigator Name,James Sellu,," "Project Name,RAMS Whole Genome Expression Profiling,," "Experiment Name,Chip 1,,"
[5] "Date,31/05/2013,," "[Data],,," "Sample_Name,Sample_Group,Sentrix_ID,Sentrix_Position" "RAMS06012,poor,9259561003,A"
[9] "RAMS12038,good,9259561003,B" "RAMS12001,good,9259561003,C" "RAMS21004,poor,9259561003,D" "RAMS12039,poor,9259561003,E"
[13] "RAMS12016,good,9259561003,F" "RAMS12032,good,9259561003,G" "RAMS12041,poor,9259561003,H" "RAMS15003,poor,9259561003,I"
[17] "RAMS20020,good,9259561003,J" "RAMS20022,good,9259561003,K" "RAMS10025,poor,9259561003,L"
> data <- readIllumina("data/9259561003", sampleSheet = sampleSheetFile, useImages = FALSE, illuminaAnnotation = "Humanv4")
Sample Sheet D:\work\RAMS\data\9259561003\sampleSheet.csv will be used to read the data
Error in analyseDirectory(dir = x, sectionNames = as.character(dirs[[x]]), :
Directory does not exist.
The only way i managed to get data into beadarray was after modifying the sampleSheet as i described earlier.
Best wishes,
Darren
-----Original Message-----
From: Mark Dunning [mailto:mark.dunning at gmail.com]
Sent: 06 June 2013 13:38
To: Darren Plant
Cc: bioconductor at stat.math.ethz.ch
Subject: Re: [BioC] beadarray - combining swath files
Hi Darren,
What directory are you running that command from?
Mark
On Thu, Jun 6, 2013 at 1:15 PM, Darren Plant <Darren.Plant at manchester.ac.uk> wrote:
Dear Mark,
I tried this originally as i hadn't read that the sampleSheet would require modification in the documentation you provide. However, I couldn't get any data in to beadarray without changing the sample sheet (error below). Is there something fundamental that I'm doing wrong? Would it be possible for me to share a section array with you to see if you can use import/summarize at your end? Thank you for your continued support, this has been a real struggle for me.
Best wishes,
Darren
> sampleSheetFile <- paste("data/9259561003", "/sampleSheet.csv", sep = "")
> readLines(sampleSheetFile)
[1] "[Header],,,"
[2] "Investigator Name,James Sellu,,"
[3] "Project Name,RAMS Whole Genome Expression Profiling,,"
[4] "Experiment Name,Chip 1,,"
[5] "Date,31/05/2013,,"
[6] "[Data],,,"
[7] "Sample_Name,Sample_Group,Sentrix_ID,Sentrix_Position"
[8] "RAMS06012,poor,9259561003,A"
[9] "RAMS12038,good,9259561003,B"
[10] "RAMS12001,good,9259561003,C"
[11] "RAMS21004,poor,9259561003,D"
[12] "RAMS12039,poor,9259561003,E"
[13] "RAMS12016,good,9259561003,F"
[14] "RAMS12032,good,9259561003,G"
[15] "RAMS12041,poor,9259561003,H"
[16] "RAMS15003,poor,9259561003,I"
[17] "RAMS20020,good,9259561003,J"
[18] "RAMS20022,good,9259561003,K"
[19] "RAMS10025,poor,9259561003,L"
> data <- readIllumina("data", sampleSheet = sampleSheetFile, useImages = FALSE, illuminaAnnotation = "Humanv4")
Sample Sheet /home/mdehsdp4/RAMS/data/9259561003/sampleSheet.csv will be used to read the data
Data for section 9259561003_A not found
Data for section 9259561003_B not found
Data for section 9259561003_C not found
Data for section 9259561003_D not found
Data for section 9259561003_E not found
Data for section 9259561003_F not found
Data for section 9259561003_G not found
Data for section 9259561003_H not found
Data for section 9259561003_I not found
Data for section 9259561003_J not found
Data for section 9259561003_K not found
Data for section 9259561003_L not found
Error in analyseDirectory(dir = x, sectionNames = as.character(dirs[[x]]), :
No data found for the specified sections
-----Original Message-----
From: Mark Dunning [mailto:mark.dunning at gmail.com]
Sent: 06 June 2013 13:02
To: Darren Plant
Cc: bioconductor at stat.math.ethz.ch
Subject: Re: [BioC] beadarray - combining swath files
Hi Darren,
You don't need to include each swath as a separate line in the sample sheet. i.e. have 12 rows with the sentrix position as A to L. beadarray should be able to detect that there are two swathes per array.
Hope this helps,
Mark
On Thu, Jun 6, 2013 at 9:11 AM, Darren Plant <Darren.Plant at manchester.ac.uk> wrote:
Dear Mark,
Please see below for a copy of the commands i used. Unfortunately I'm still getting the same problem following your suggestion.
Best wishes,
Darren
> processSwathData(inputDir = "data/9259561003", outputDir = "data/9259561003", twoColour=NULL, textstring="_perBeadFile.txt", segmentHeight=326, segmentWidth=397, fullOutput=TRUE, newTextString="_Grn.txt")
> sampleSheetFile <- paste("data/9259561003", "/sampleSheet.csv", sep = "")
> readLines(sampleSheetFile)
[1] "[Header],,," "Investigator Name,,,"
[3] "Project Name,RMS Whole Genome Expression Profiling,," "Experiment Name,,,"
[5] "Date,31/05/2013,," "[Data],,,"
[7] "Sample_Name,Sample_Group,Sentrix_ID,Sentrix_Position" "RAMS06012,poor,9259561003,A-Swath1_Grn"
[9] "RM06012,poor,9259561003,A-Swath2_Grn" "RM12038,good,9259561003,B-Swath1_Grn"
[11] "RM12038,good,9259561003,B-Swath2_Grn" "RM12001,good,9259561003,C-Swath1_Grn"
[13] "RM12001,good,9259561003,C-Swath2_Grn" "RM21004,poor,9259561003,D-Swath1_Grn"
[15] "RM21004,poor,9259561003,D-Swath2_Grn" "RM12039,poor,9259561003,E-Swath1_Grn"
[17] "RM12039,poor,9259561003,E-Swath2_Grn" "RM12016,good,9259561003,F-Swath1_Grn"
[19] "RM12016,good,9259561003,F-Swath2_Grn" "RM12032,good,9259561003,G-Swath1_Grn"
[21] "RM12032,good,9259561003,G-Swath2_Grn" "RM12041,poor,9259561003,H-Swath1_Grn"
[23] "RM12041,poor,9259561003,H-Swath2_Grn" "RM15003,poor,9259561003,I-Swath1_Grn"
[25] "RM15003,poor,9259561003,I-Swath2_Grn" "RM20020,good,9259561003,J-Swath1_Grn"
[27] "RM20020,good,9259561003,J-Swath2_Grn" "RM20022,good,9259561003,K-Swath1_Grn"
[29] "RM20022,good,9259561003,K-Swath2_Grn" "RM10025,poor,9259561003,L-Swath1_Grn"
[31] "RM10025,poor,9259561003,L-Swath2_Grn"
> data <- readIllumina("data", sampleSheet = sampleSheetFile, useImages = FALSE, illuminaAnnotation = "Humanv4")
Sample Sheet D:\work\RAMS\data\9259561003\sampleSheet.csv will be used to read the data
Processing section 9259561003_A-Swath1_Grn
Processing section 9259561003_A-Swath2_Grn
Processing section 9259561003_B-Swath1_Grn
Processing section 9259561003_B-Swath2_Grn
Processing section 9259561003_C-Swath1_Grn
Processing section 9259561003_C-Swath2_Grn
Processing section 9259561003_D-Swath1_Grn
Processing section 9259561003_D-Swath2_Grn
Processing section 9259561003_E-Swath1_Grn
Processing section 9259561003_E-Swath2_Grn
Processing section 9259561003_F-Swath1_Grn
Processing section 9259561003_F-Swath2_Grn
Processing section 9259561003_G-Swath1_Grn
Processing section 9259561003_G-Swath2_Grn
Processing section 9259561003_H-Swath1_Grn
Processing section 9259561003_H-Swath2_Grn
Processing section 9259561003_I-Swath1_Grn
Processing section 9259561003_I-Swath2_Grn
Processing section 9259561003_J-Swath1_Grn
Processing section 9259561003_J-Swath2_Grn
Processing section 9259561003_K-Swath1_Grn
Processing section 9259561003_K-Swath2_Grn
Processing section 9259561003_L-Swath1_Grn
Processing section 9259561003_L-Swath2_Grn
datasumm <- summarize(data,useSampleFac=T,sampleFac=rep(1:12,each=2))
Finding list of unique probes in beadLevelData
48324 unique probeIDs found
Number of unmapped probes removed: 217 Summarizing G channel Processing Array 1 Summarizing G channel Processing Array 2 Removing outliers Using exprFun Using varFun Summarizing G channel Processing Array 3 Summarizing G channel Processing Array 4 Removing outliers Using exprFun Using varFun Summarizing G channel Processing Array 5 Summarizing G channel Processing Array 6 Removing outliers Using exprFun Using varFun Summarizing G channel Processing Array 7 Summarizing G channel Processing Array 8 Removing outliers Using exprFun Using varFun Summarizing G channel Processing Array 9 Summarizing G channel Processing Array 10 Removing outliers Using exprFun Using varFun Summarizing G channel Processing Array 11 Summarizing G channel Processing Array 12 Removing outliers Using exprFun Using varFun Summarizing G channel Processing Array 13 Summarizing G channel Processing Array 14 Removing outliers Using exprFun Using varFun Summarizing G channel Processing Array 15 Summarizing G channel Processing Array 16 Removing outliers Using exprFun Using varFun Summarizing G channel Processing Array 17 Summarizing G channel Processing Array 18 Removing outliers Using exprFun Using varFun Summarizing G channel Processing Array 19 Summarizing G channel Processing Array 20 Removing outliers Using exprFun Using varFun Summarizing G channel Processing Array 21 Summarizing G channel Processing Array 22 Removing outliers Using exprFun Using varFun Summarizing G channel Processing Array 23 Summarizing G channel Processing Array 24 Removing outliers Using exprFun Using varFun Making summary object Annotating control probes using package illuminaHumanv4.db Version:1.16.0
Error in value[[3L]](cond) : row names supplied are of the wrong length
AnnotatedDataFrame 'initialize' could not update varMetadata:
perhaps pData and varMetadata are inconsistent?
-----Original Message-----
From: Mark Dunning [mailto:mark.dunning at gmail.com]
Sent: 05 June 2013 15:45
To: Darren Plant
Cc: bioconductor at stat.math.ethz.ch
Subject: Re: [BioC] beadarray - combining swath files
Hi Darren,
I'm having a little trouble trying to reproduce the error. What commands did you use to generate the bead-level data? It seems to work for the data that I have.
In the meantime, you can force beadarray to consolidate sections by using the sampleFac argument. The resulting object will then have all columns (samples).
> bsd <- summarize(bld,useSampleFac=T,sampleFac=rep(1:12,each=2))
> bsd
ExpressionSetIllumina (storageMode: list)
assayData: 48107 features, 12 samples
element names: exprs, se.exprs, nObservations
protocolData: none
phenoData
rowNames: 8106854095_A 8106854095_B ... 8106854095_L (12 total)
varLabels: sampleID SampleFac
varMetadata: labelDescription
featureData
featureNames: ILMN_1802380 ILMN_1893287 ... ILMN_1806862 (48107
total)
fvarLabels: ArrayAddressID IlluminaID Status
fvarMetadata: labelDescription
experimentData: use 'experimentData(object)'
Annotation: Humanv4
QC Information
Available Slots:
QC Items: Date, Beadchip, ..., SampleGroup, numBeads
sampleNames: 8106854095_A-Swath1, 8106854095_A-Swath2, ..., 8106854095_L-Swath1, 8106854095_L-Swath2
Please send me your code though.
Regards,
Mark
On Wed, Jun 5, 2013 at 9:43 AM, Darren <darren.plant at manchester.ac.uk> wrote:
Sunitha M <sunkorner at ...> writes:
>
> Dear all,
>
> I am trying to analyse Illumina beadarray data produced by iScan for the
first time. This scanner saves each
> array in two different tiff images. As a first step, I used
ProcessSwathData() function that
> deconvolutes the bead-level data and creates two files, swath1 and
swath2 for the two tiff images.
> However, in the subsequent step, i. e. readIllumina function these two
files are treated as if they are
> from two different arrays (although they belong to one array). Is there
any parameter we can pass to the
> readIllumina function to indicate that those two files belongs to one
array.
>
> Any help in this regard is highly appreciated.
>
> Thanks
>
> Sunitha
>
> [[alternative HTML version deleted]]
>
>
> Dear Sunitha,
i hope you don't mind me joining in but i am faced with the same problem.
There is no information on how to proceed with iScan data after
ProcessSwathData() as far as i can see. Please let me know if you figure
this out. I think others have used Illumina software to process the tiff
files as an alternative.
Best wishes,
Darren
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