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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