Hi! I am trying to analyze some GEO data and have been facing download problems which I was able to fix by reading recent postings on this list. But something goes wrong when I try to convert to an MAList. I suspect it could have something to do with the fact that this particular data series comprizes two different platforms. Here the transcript of what I do: ------------------------------------------------------------------- require(GEOquery) options(download.file.method="wget") # fix download problem dat <- getGEO(filename='data/GSE6794_family.soft.gz', destdir=datapath, GSEMatrix=F) # [...] some logging output, no errors or warnings MA <- GDS2MA(dat,do.log2=T) Loading required package: limma File stored at: /tmp/RtmpvL1wBp/GPL75.annot.gz/tmp/RtmpvL1wBp/GPL76.annot.gz Error in function (classes, fdef, mtable) : unable to find an inherited method for function "Table", for signature "GSE" In addition: Warning messages: 1: In if (GSEMatrix & geotype == "GSE") { : the condition has length > 1 and only the first element will be used 2: In if (geotype == "GDS") { : the condition has length > 1 and only the first element will be used 3: In if (geotype == "GSE" & amount == "full") { : the condition has length > 1 and only the first element will be used 4: In if (geotype == "GSE" & amount != "full" & amount != "table") { : the condition has length > 1 and only the first element will be used 5: In if (geotype == "GPL") { : the condition has length > 1 and only the first element will be used 6: In if (geotype == "GSM") { : the condition has length > 1 and only the first element will be used 7: In if (!file.exists(destfile)) { : the condition has length > 1 and only the first element will be used 8: In gzfile(fname, open = "rt") : only first element of 'description' argument used 9: In gzfile(fname, open = "rt") : only first element of 'description' argument used sessionInfo() R version 2.11.1 (2010-05-31) x86_64-pc-linux-gnu locale: [1] LC_CTYPE=en_US.utf8 LC_NUMERIC=C LC_TIME=en_US.utf8 LC_COLLATE=en_US.utf8 [5] LC_MONETARY=C LC_MESSAGES=en_US.utf8 LC_PAPER=en_US.utf8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C LC_MEASUREMENT=en_US.utf8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics utils datasets grDevices methods base other attached packages: [1] limma_3.4.0 GEOquery_2.13.5 Biobase_2.8.0 lattice_0.18-8 loaded via a namespace (and not attached): [1] grid_2.11.1 RCurl_1.4-2 XML_3.1-0 ------------------------------------------------------------------- I can use GSMList to extract a list with all GSM entries but, of course, GDS2MA will not work on a list and I would have to run it on all list members individually which I will have to re-assemble into a single MA object somehow... Any hints welcome. cu Philipp -- Dr. Philipp Pagel Lehrstuhl f?r Genomorientierte Bioinformatik Technische Universit?t M?nchen Wissenschaftszentrum Weihenstephan Maximus-von-Imhof-Forum 3 85354 Freising, Germany http://webclu.bio.wzw.tum.de/~pagel/

On Thu, Jul 29, 2010 at 11:00 AM, Philipp Pagel <p.pagel@wzw.tum.de> wrote: > > Hi! > > I am trying to analyze some GEO data and have been facing download problems > which I was able to fix by reading recent postings on this list. But > something > goes wrong when I try to convert to an MAList. I suspect it could have > something to do with the fact that this particular data series comprizes > two > different platforms. > > Here the transcript of what I do: > > ------------------------------------------------------------------- > require(GEOquery) > options(download.file.method="wget") # fix download problem > dat <- getGEO(filename='data/GSE6794_family.soft.gz', destdir=datapath, > GSEMatrix=F) > # [...] some logging output, no errors or warnings > > MA <- GDS2MA(dat,do.log2=T) > Hi, Philipp. GDS2MA is for converting a GDS object to an MAList. It will not work for a GSE object, which is what you will get back from the getGEO() with GSEMatrix=FALSE. I would suggest doing using: dat <- getGEO('GSE6794') You will then have a list of two ExpressionSets (if there are two platforms in the GSE). You can then use the convert package to convert each of those to an MAList. Hope that helps. Sean > Loading required package: limma > File stored at: > /tmp/RtmpvL1wBp/GPL75.annot.gz/tmp/RtmpvL1wBp/GPL76.annot.gz > Error in function (classes, fdef, mtable) : > unable to find an inherited method for function "Table", for signature > "GSE" > In addition: Warning messages: > 1: In if (GSEMatrix & geotype == "GSE") { : > the condition has length > 1 and only the first element will be used > 2: In if (geotype == "GDS") { : > the condition has length > 1 and only the first element will be used > 3: In if (geotype == "GSE" & amount == "full") { : > the condition has length > 1 and only the first element will be used > 4: In if (geotype == "GSE" & amount != "full" & amount != "table") { : > the condition has length > 1 and only the first element will be used > 5: In if (geotype == "GPL") { : > the condition has length > 1 and only the first element will be used > 6: In if (geotype == "GSM") { : > the condition has length > 1 and only the first element will be used > 7: In if (!file.exists(destfile)) { : > the condition has length > 1 and only the first element will be used > 8: In gzfile(fname, open = "rt") : > only first element of 'description' argument used > 9: In gzfile(fname, open = "rt") : > only first element of 'description' argument used > > sessionInfo() > R version 2.11.1 (2010-05-31) > x86_64-pc-linux-gnu > > locale: > [1] LC_CTYPE=en_US.utf8 LC_NUMERIC=C LC_TIME=en_US.utf8 > LC_COLLATE=en_US.utf8 > [5] LC_MONETARY=C LC_MESSAGES=en_US.utf8 > LC_PAPER=en_US.utf8 LC_NAME=C > [9] LC_ADDRESS=C LC_TELEPHONE=C > LC_MEASUREMENT=en_US.utf8 LC_IDENTIFICATION=C > > attached base packages: > [1] stats graphics utils datasets grDevices methods base > > other attached packages: > [1] limma_3.4.0 GEOquery_2.13.5 Biobase_2.8.0 lattice_0.18-8 > > loaded via a namespace (and not attached): > [1] grid_2.11.1 RCurl_1.4-2 XML_3.1-0 > ------------------------------------------------------------------- > > > I can use GSMList to extract a list with all GSM entries but, of course, > GDS2MA > will not work on a list and I would have to run it on all list members > individually which I will have to re-assemble into a single MA object > somehow... Any hints welcome. > > cu > Philipp > > -- > Dr. Philipp Pagel > Lehrstuhl für Genomorientierte Bioinformatik > Technische Universität München > Wissenschaftszentrum Weihenstephan > Maximus-von-Imhof-Forum 3 > 85354 Freising, Germany > http://webclu.bio.wzw.tum.de/~pagel/ > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > [[alternative HTML version deleted]]