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

On Thu, Feb 26, 2009 at 4:42 PM, Pan Du <dupan@northwestern.edu> wrote:

>  Yes, you can use produceGEOPlatformFile, but this function has not been
> well tested.
>
>
> Pan
>
> On 2/26/09 3:38 PM, "ss" <affysnp@gmail.com> wrote:
>
> Thank you, Pan. I am grateful to your help!
> So for the new platform, I can basically use
> the one generated by produceGEOPlatformFile?
>
> Regards,
>      Allen
>
>

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