Entering edit mode
Pan Du
★
1.2k
@pan-du-2010
Last seen 10.3 years ago
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
file:
## 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',
sampleInfo='GEOsampleInfo.txt')
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,
Pan
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
>
>
>