If I use GEOquery as follows: gse <- getGEO("GSE21259", GSEMatrix=TRUE) I get the following warnings after the load: Warning messages: 1: In read.table(con, sep = "\t", header = FALSE, nrows = nseries) : seek on a gzfile connection returned an internal error 2: In read.table(con, sep = "\t", header = FALSE, nrows = nsamples) : seek on a gzfile connection returned an internal error 3: In readLines(con, 1) : seek on a gzfile connection returned an internal error 4: In read.table(file = file, header = header, sep = sep, ... : seek on a gzfile connection returned an internal error 5: In read.table(file = file, header = header, sep = sep, ... : seek on a gzfile connection returned an internal error 6: In read.table(con, sep = "\t", header = FALSE, nrows = nseries) : seek on a gzfile connection returned an internal error 7: In read.table(con, sep = "\t", header = FALSE, nrows = nsamples) : seek on a gzfile connection returned an internal error 8: In readLines(con, 1) : seek on a gzfile connection returned an internal error 9: In read.table(file = file, header = header, sep = sep, ... : seek on a gzfile connection returned an internal error 10: In read.table(file = file, header = header, sep = sep, ... : seek on a gzfile connection returned an internal error 11: In read.table(con, sep = "\t", header = FALSE, nrows = nseries) : seek on a gzfile connection returned an internal error 12: In read.table(con, sep = "\t", header = FALSE, nrows = nsamples) : seek on a gzfile connection returned an internal error 13: In readLines(con, 1) : seek on a gzfile connection returned an internal error 14: In read.table(file = file, header = header, sep = sep, ... : seek on a gzfile connection returned an internal error 15: In read.table(file = file, header = header, sep = sep, ... : seek on a gzfile connection returned an internal error Then things that should work don't, i.e.: > GPLList(gse) Error in function (classes, fdef, mtable) : unable to find an inherited method for function "GPLList", for signature "list" > GSMList(gse) Error in function (classes, fdef, mtable) : unable to find an inherited method for function "GSMList", for signature "list" (1) Am I doing something wrong? (2) Is this data set on GEO broken in some way? (3) Or is it a bioconductor error? -- output of sessionInfo(): R version 2.13.2 (2011-09-30) Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit) locale: [1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] GEOquery_2.19.4 Biobase_2.12.2 loaded via a namespace (and not attached): [1] RCurl_1.6-10 XML_3.4-3 -- Sent via the guest posting facility at bioconductor.org.

Hi, Shawn. On Thu, Oct 13, 2011 at 4:21 PM, Shawn Garbett [guest] < guest@bioconductor.org> wrote: > > If I use GEOquery as follows: > > gse <- getGEO("GSE21259", GSEMatrix=TRUE) > > I get the following warnings after the load: > > Warning messages: > 1: In read.table(con, sep = "\t", header = FALSE, nrows = nseries) : > seek on a gzfile connection returned an internal error > 2: In read.table(con, sep = "\t", header = FALSE, nrows = nsamples) : > seek on a gzfile connection returned an internal error > 3: In readLines(con, 1) : seek on a gzfile connection returned an internal > error > 4: In read.table(file = file, header = header, sep = sep, ... : > seek on a gzfile connection returned an internal error > 5: In read.table(file = file, header = header, sep = sep, ... : > seek on a gzfile connection returned an internal error > 6: In read.table(con, sep = "\t", header = FALSE, nrows = nseries) : > seek on a gzfile connection returned an internal error > 7: In read.table(con, sep = "\t", header = FALSE, nrows = nsamples) : > seek on a gzfile connection returned an internal error > 8: In readLines(con, 1) : seek on a gzfile connection returned an internal > error > 9: In read.table(file = file, header = header, sep = sep, ... : > seek on a gzfile connection returned an internal error > 10: In read.table(file = file, header = header, sep = sep, ... : > seek on a gzfile connection returned an internal error > 11: In read.table(con, sep = "\t", header = FALSE, nrows = nseries) : > seek on a gzfile connection returned an internal error > 12: In read.table(con, sep = "\t", header = FALSE, nrows = nsamples) : > seek on a gzfile connection returned an internal error > 13: In readLines(con, 1) : seek on a gzfile connection returned an internal > error > 14: In read.table(file = file, header = header, sep = sep, ... : > seek on a gzfile connection returned an internal error > 15: In read.table(file = file, header = header, sep = sep, ... : > seek on a gzfile connection returned an internal error > > The warning messages are just that. Things will work fine even with the warnings. > Then things that should work don't, i.e.: > > > GPLList(gse) > Error in function (classes, fdef, mtable) : > unable to find an inherited method for function "GPLList", for signature > "list" > > GSMList(gse) > Error in function (classes, fdef, mtable) : > unable to find an inherited method for function "GSMList", for signature > "list" > > (1) Am I doing something wrong? > (2) Is this data set on GEO broken in some way? > (3) Or is it a bioconductor error? > > You've got it most of the way. The output of getGEO for a GSE when GSEMatrix=TRUE is a *list* of ExpressionSets. Try this: names(gse) gseEset = gse[[1]] gseEset You'll notice that gseEset is an ExpressionSet, so all the usual ExpressionSet stuff "just works". Hopefully that clarifies things. Sean P.S. Thanks for sessionInfo(). > -- output of sessionInfo(): > > R version 2.13.2 (2011-09-30) > Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit) > > locale: > [1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8 > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] GEOquery_2.19.4 Biobase_2.12.2 > > loaded via a namespace (and not attached): > [1] RCurl_1.6-10 XML_3.4-3 > > -- > Sent via the guest posting facility at bioconductor.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]]