Hi Pan,

I have tried the code you provided and got the submissionFile like:

#ID_REF =
#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    VALUE    RAW_VALUE    BEAD_STDERR    Detection_Pval    Avg_NBEADS
ILMN_10000    7.67644911129066    81.2483    6.9638    0.997088792    41
ILMN_100000    6.89318565949701    0.3596772    2.239353    0.5924309    40

However, GEO would rather have unique identifiers as Illumina recently made.
They gave me an example as shown in:

http://www.ncbi.nlm.nih.gov/projects/geo/query/acc.cgi?acc=GPL6887

I see what they say and understand that the so-called unique identifiers are
of the same length, in contrast to earlier identifiers such as:

ILMN_10000
ILMN_100000

which I got.

I am not sure whether lumi could accomplish this. Or the alternative way
GEO could accept is to use nuID.

But as an example I showed in my last email, the nuID in the
GEOSubmissionFIle
is in the second column, which won't match the ID column in PlatformFile.

Any ideas?

Best,
     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
>
>

	[[alternative HTML version deleted]]

