Dear list, I can't seem to get the GSElimits parameters of the GEOquery getGEO function to work, it seems to be ignored as the full dataset is always returned. Many thanks. James. library("GEOquery") softFile <- system.file("extdata/GSE781_family.soft.gz", package = "GEOquery") ## full set gse <- getGEO(filename = softFile) Parsing.... Found 36 entities... GPL96 (1 of 36 entities) GPL97 (2 of 36 entities) GSM11805 (3 of 36 entities) etc.. ## reduced set (samples 1 to 5) gseSub <- getGEO(filename = softFile, GSElimits = c(1, 5)) Parsing.... Found 36 entities... GPL96 (1 of 36 entities) GPL97 (2 of 36 entities) GSM11805 (3 of 36 entities) etc.. length(names(GSMList(gse))) [1] 34 length(names(GSMList(gseSub))) [1] 34 > sessionInfo() R version 2.12.0 (2010-10-15) Platform: x86_64-pc-linux-gnu (64-bit) locale: [1] LC_CTYPE=en_US.utf8 LC_NUMERIC=C [3] LC_TIME=en_US.utf8 LC_COLLATE=en_US.utf8 [5] LC_MONETARY=C LC_MESSAGES=en_US.utf8 [7] LC_PAPER=en_US.utf8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.utf8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets tools methods [8] base other attached packages: [1] GEOquery_2.16.1 Biobase_2.10.0 loaded via a namespace (and not attached): [1] RCurl_1.5-0 XML_3.2-0

On Fri, Dec 17, 2010 at 8:28 AM, James F. Reid < james.reid@ifom-ieo-campus.it> wrote: > Dear list, > > I can't seem to get the GSElimits parameters of the GEOquery getGEO > function to work, it seems to be ignored as the full dataset is always > returned. > > Thanks, James, for the very clear report of the problem. I have fixed this in both the Release (v2.16.2) and Devel branches (v2.17.2). The changes should move through the build system in a day or two. Sean > Many thanks. > James. > > library("GEOquery") > > softFile <- system.file("extdata/GSE781_family.soft.gz", package = > "GEOquery") > > ## full set > gse <- getGEO(filename = softFile) > Parsing.... > Found 36 entities... > GPL96 (1 of 36 entities) > GPL97 (2 of 36 entities) > GSM11805 (3 of 36 entities) > etc.. > > ## reduced set (samples 1 to 5) > gseSub <- getGEO(filename = softFile, GSElimits = c(1, 5)) > Parsing.... > Found 36 entities... > GPL96 (1 of 36 entities) > GPL97 (2 of 36 entities) > GSM11805 (3 of 36 entities) > etc.. > > > length(names(GSMList(gse))) > [1] 34 > length(names(GSMList(gseSub))) > [1] 34 > > > sessionInfo() > R version 2.12.0 (2010-10-15) > Platform: x86_64-pc-linux-gnu (64-bit) > > locale: > [1] LC_CTYPE=en_US.utf8 LC_NUMERIC=C > [3] LC_TIME=en_US.utf8 LC_COLLATE=en_US.utf8 > [5] LC_MONETARY=C LC_MESSAGES=en_US.utf8 > [7] LC_PAPER=en_US.utf8 LC_NAME=C > [9] LC_ADDRESS=C LC_TELEPHONE=C > [11] LC_MEASUREMENT=en_US.utf8 LC_IDENTIFICATION=C > > attached base packages: > [1] stats graphics grDevices utils datasets tools methods > [8] base > > other attached packages: > [1] GEOquery_2.16.1 Biobase_2.10.0 > > loaded via a namespace (and not attached): > [1] RCurl_1.5-0 XML_3.2-0 > > _______________________________________________ > 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]]