Geo GDS parser availability

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Sean Davis 21k

@sean-davis-490

Last seen 3 months ago

United States

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

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ADD COMMENT • link updated 18.7 years ago by Saurin D. Jani ▴ 360 • written 18.7 years ago by Sean Davis 21k

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John Zhang ★ 2.9k

@john-zhang-6

Last seen 9.6 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

ADD COMMENT • link 18.7 years ago John Zhang ★ 2.9k

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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

ADD REPLY • link 18.7 years ago Sean Davis 21k

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Saurin D. Jani ▴ 360

@saurin-d-jani-944

Last seen 9.6 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 > >

ADD COMMENT • link 18.7 years ago Saurin D. Jani ▴ 360

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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

ADD REPLY • link 18.7 years ago Sean Davis 21k

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