Hi Pan,

Thanks so much.

Just a little bit updates for you by our conversations with folks in GEO.

They suggest that the platform needs to be in the same file of
submissionFile
as the samples+series (as a family with all three entities), like this:

http://www.ncbi.nlm.nih.gov/projects/geo/info/soft_ex_family.txt

Please note that they also want a new series session at the very end of
the submissionFile.

(1) About the platformFile, I just came up with this code to make a
platformFile:

#####code for Platform###################
probeList<-rownames(exprs(john3))
Symbol<-mget(probeList,lumiHumanAllSYMBOL,ifnotfound = NA)
ENTREZID<-mget(probeList,lumiHumanAllENTREZID,ifnotfound = NA)
illuminaID = nuID2IlluminaID(featureNames(john3), species="Human",
idType="Gene")
probeID=nuID2probeID(probeList, lib.mapping = "lumiHumanIDMapping")
anno=cbind(illuminaID=illuminaID,
illuminaProbeID=probeID,Symbol=as.character(Symbol),ENTREZID=as.character(ENTREZID))
write.table(anno, file="sue_6_processed_data_symbol.txt",sep = "\t",quote =
FALSE)

And then I just added some header information as required.

(2) I have a question again about produceGEOSubmissionFile(). I cut the few
first rows
in the GEOSubmissionFile(). My question is how I could make the nuID as the
first column.

#ID_REF =
#nuID = nucleotide universal IDentifier (nuID), convertible to and from
probe sequence. See Bioconductor lumi package for more details.
#VALUE = normalized signal intensity
#RAW_VALUE = raw signal intensity
#BEAD_STDERR = the standard error of the probe measurements
#Detection_Pval = the detection p-value of the probe
#Avg_NBEADS = Number of beads for the probe
!sample_table_begin
ID_REF    nuID    VALUE    RAW_VALUE    BEAD_STDERR    Detection_Pval
Avg_NBEADS
0006960451    NQqs8dKRwVSgI4SRPk    7.67644911129066    81.2483    6.9638
0.997088792    41
0002850504    ERVJG9FehRAB6AoIq0    6.89318565949701    0.3596772
2.239353    0.5924309    40

I will try the code you suggest very soon.

Thanks a lot!

Sincerely,
       Allen




On Fri, Feb 27, 2009 at 4:48 PM, Pan Du <dupan@northwestern.edu> wrote:

>  Hi Allen,
>
> After I checked the LumiBatch object you sent me, I found the original
> Illumina IDs were kept in the featureData of LumiBatch object.
> In this case, you can retrieve this Illumina ID and create the GEO
> submission file.
>
> Here is some example code:
> ## suppose lumiRaw and lumiNormalized are LumiBatch objects keeping the
> raw data and normalized data, respectively, and "sampleInfoFile.txt" keeps
> the sample information
> > fd = pData(featureData(lumiRaw))
> > featureNames( lumiRaw) <- featureNames( lumiNormalized ) <- fd$TargetID
> >
> > produceGEOSubmissionFile(lumiNormalized, lumiRaw,  sampleInfo =
> "sampleInfoFile.txt")
>
>
> Pan
>
>
> On 2/27/09 11:41 AM, "ss" <affysnp@gmail.com> wrote:
>
> Hi Pan,
>
> Obviously I am writing back to you again for help. A lot of hurdles
> have been cleared by working with folks in GEO except that the IDs
> in the platform table are not unique.
>
> ID    Illumina_ProbeID    Illumina_Gene    lumiID    Search_Key
> Accession    Symbol    ProbeSequence
>
> ILMN_30605    1230152    ILMN_30605    iDuqkUgmpFvie_Qe94    ILMN_30605
> XM_933328.1    LOC643918
> AATGTGGGGGCACCAGAAGCGGGCACCGTTGAGCTGTTGCAACTGTTCTG
>
> ILMN_30605    7160612    ILMN_30605    W8CdwN0.UfI.w75PsE    ILMN_30605
> XM_933328.1    LOC643918
> TTAAAGCTCTAAATCTCATTTCCACTTAGATTTTAATGTTGCATTGTAAC
>
> As you can see, there are two "ILMN_30605" IDs. I guess that is due to the
> library argument
> I have used in produceGEOPlatformFile function:
>
> produceGEOPlatformFile(john, lib.mapping = 'lumiHumanIDMapping', nuIDMode =
> FALSE, fileName = "GEOPlatformFile.txt")
>
> We originally have 46713 probes, but we end up with getting 48701 probes in
> the PlatformFile.
> How can I fix this?
>
> Thank you so much!
>
> Allen
>
>

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