Entering edit mode
Not entirely BioConductor related, but I'll ask:
Does anyone know of a GEO (gene expression omnibus) GDS parser (R,
perl, or otherwise)?
Thanks,
Sean
0
Entering edit mode
John Zhang
★
2.9k
@john-zhang-6
Last seen 10.3 years ago
>Does anyone know of a GEO (gene expression omnibus) GDS parser (R,
>perl, or otherwise)?
AnnBuilder has something that reads a file from GEO into R.
>library(AnnBuilder)
>geo <- GEO()
>temp <- queryGEO(geo, "GPL49")
Not sure if this is what you want.
>
>Thanks,
>Sean
>
>_______________________________________________
>Bioconductor mailing list
>Bioconductor at stat.math.ethz.ch
>https://stat.ethz.ch/mailman/listinfo/bioconductor
Jianhua Zhang
Department of Medical Oncology
Dana-Farber Cancer Institute
44 Binney Street
Boston, MA 02115-6084
0
Entering edit mode
On Jul 27, 2005, at 2:25 PM, John Zhang wrote:
>
> >Does anyone know of a GEO (gene expression omnibus) GDS parser (R,
> >perl, or otherwise)?
>
> AnnBuilder has something that reads a file from GEO into R.
> >library(AnnBuilder)
> >geo <- GEO()
> >temp <- queryGEO(geo, "GPL49")
>
> Not sure if this is what you want.
Jianhua,
I was aware of this one, but actually, I am looking for one that reads
the GDS files, not GPL files.
Thanks,
Sean
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19.4 years ago
Sean Davis
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Entering edit mode
Saurin D. Jani
▴
360
@saurin-d-jani-944
Last seen 10.3 years ago
Hi Sean,
Try to see on this page:
http://proteogenomics.musc.edu/quickSite/arrayQuest.php?page=home&act=
manage&process=Methods_Library_List
Method number 14 does GEO analysis for TWO condition experiment and it
also
parses GDS SOFT file. There is an R script.
Saurin
Quoting Sean Davis <sdavis2 at="" mail.nih.gov="">:
> Not entirely BioConductor related, but I'll ask:
>
> Does anyone know of a GEO (gene expression omnibus) GDS parser (R,
> perl, or otherwise)?
>
> Thanks,
> Sean
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor
>
>
0
Entering edit mode
On Jul 27, 2005, at 3:06 PM, Saurin D. Jani wrote:
> Hi Sean,
>
> Try to see on this page:
> http://proteogenomics.musc.edu/quickSite/arrayQuest.php?
> page=home&act=manage&process=Methods_Library_List
>
> Method number 14 does GEO analysis for TWO condition experiment and
it
> also
> parses GDS SOFT file. There is an R script.
Thanks, Saurin. That will be helpful.
Sean
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