Hi Allen,

If your data is nuID identified and you set parameter lib.mapping as NULL,
you will get the GEO submission file with nuID as ID_REF.
In this case, you platform should also be nuID identified.

> produceGEOSubmissionFile(lumiNormalized, lumiRaw, lib.mapping=NULL, sampleInfo
= "sampleInfoFile.txt")


Pan


On 2/27/09 4:28 PM, "ss" <affysnp@gmail.com> wrote:

> 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(ENTR
> EZID))
> 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
> 
> 


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