On Fri, Oct 5, 2012 at 1:40 PM, Sylvain Foisy <sylvain.foisy@inflammgen.org>wrote: > Hi, > > I am so not a R expert so I apologize for the newbie question... If I have > a list of gene symbols, can I get, for each of them, all GEO profiles for > that gene across all platforms (or a subset of), extract normalized gene > expression for that gene and feed this to LIMMA or the like to observe > differential expression and make a list of all Datasets where this gene is > differentially expressed? > > Hi, Sylvain. Sorry for the late reply. You can use GEOquery to download entire datasets as you see fit. As for differential expression, that is trickier since you will need to define a way to examine the metadata for each GEO dataset to determine what to use for defining groups for testing for differential expression. A secondary concern is that the GEO platform files do not contain standard columns, so there is no guarantee that a gene identifier exists or how you would find such a column programmatically if it did. Sean > Sorry if this seems stupid; I promised to document any solution in our > wiki and share it with the world ;-) > > Best regards > > Sylvain > > ============================================================== > Sylvain Foisy, Ph. D. > Chargé de projet | Project Manager > Bioinformatics > Labo. de génétique et médecine génomique de l'inflammation > Centre de recherche > Institut de cardiologie de Montréal > 5000 Bélanger Est > Montréal, Qc H1T 1C8 > CANADA > > T: (514) 376-3330 x.2299 > F: 514-593-2539 > M: sylvain.foisy@inflammgen.org > W: http://inflammgen.org > ============================================================== > > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > [[alternative HTML version deleted]]