[BioC] About GEO submission of Illumina data

Pan Du dupan at northwestern.edu
Fri Jan 23 21:56:01 CET 2009

Hi Christine,

There is function "produceGEOSubmissionFile" in lumi to produce the GEO
submission file in SOFT format. Please check the latest lumi.pdf and related
help files for more details. Here is an example of producing GEO submission

## Produce the sample information template
> produceGEOSampleInfoTemplate(lumi.example, lib.mapping = 'lumiHumanIDMapping',
fileName = "GEOsampleInfo.txt")

## After editing the 'GEOsampleInfo.txt' by filling in sample information
> produceGEOSubmissionFile(lumi.N.Q, lumi.example, lib='lumiHumanIDMapping',

During editing the 'GEOsampleInfo.txt', you need to fill in the
corresponding Illumina Platform ID, which can be found at GEO website. Tell
me if you meet any problems.

Have a nice weekend,


On 1/23/09 3:09 AM, "steinhof at molgen.mpg.de" <steinhof at molgen.mpg.de> wrote:

> Dear Pan
> I am sitting here with the collaborator who generated the Illumina data and
> she
> is currently preparing the manuscript for publication. Since the complete data
> has to be stored in GEO/arrayExpress they have to submit all annotated data
> (including the Illumina probe ID from the original file).
> Unfortunately I was not able to solve the problem so far. Otherwise the
> lumipackage analysis was great and very straightforward to use and to apply.
> Below there is the email with the remaining annotation problem. I would be
> very
> greatful if you could help me in this matter. They push me since its extremely
> urgent. 
> thank you very much for your support!!!
> Best wishes
> Christine

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