Hello, I need help , I have a problem with (GEOquery) package a first of all, I can't download and this the warning message >library(GEOquery) Setting options('download.file.method.GEOquery'='curl') > gds1257 <- getGEO('GDS858', destdir=".") File stored at: ./GDS1257.soft.gz Error in read.table(con, sep = "\t", header = FALSE, nrows = nseries) : invalid 'nlines' argument > gds1257 Error: object 'gds1257' not found The second problem is : If i download the gds file manually with "wget" and after that we use the GDS2eSet i have this message : gds <- getGEO(filename='GDS1257.soft.gz') eset <- GDS2eSet(gds, do.log2=TRUE) File stored at: /tmp/RtmpY4ZgWQ/GPL96.annot.gz Error in read.table(con, sep = "\t", header = FALSE, nrows = nseries) : invalid 'nlines' argument > eset Error: object 'eset' not found waiting response , thank you very much Best Cherif [[alternative HTML version deleted]]

Hi, Cherif. You didn't include the output of sessionInfo(), so I am not sure what version of GEOquery you are using. I suspect that you are using an outdated version and need to upgrade. In any case, I am not able to reproduce your problem, so let me know if you have problems after upgrading. Sean > gds1257 = getGEO('GDS1257') File stored at: /var/folders/21/8t47kwys6vqb8606kdfn71780000gn/T//RtmpFgWQxT/GDS1257.s oft.gz > eset = GDS2eSet(gds1257) File stored at: /var/folders/21/8t47kwys6vqb8606kdfn71780000gn/T//RtmpFgWQxT/GPL96.ann ot.gz There were 30 warnings (use warnings() to see them) > eset ExpressionSet (storageMode: lockedEnvironment) assayData: 22283 features, 33 samples element names: exprs protocolData: none phenoData sampleNames: GSM32620 GSM32621 ... GSM32651 (33 total) varLabels: sample disease.state description varMetadata: labelDescription featureData featureNames: 1007_s_at 1053_at ... AFFX-TrpnX-M_at (22283 total) fvarLabels: ID Gene title ... GO:Component ID (21 total) fvarMetadata: Column labelDescription experimentData: use 'experimentData(object)' pubMedIds: 15741505 Annotation: > sessionInfo() R version 3.0.2 Patched (2014-01-22 r64855) Platform: x86_64-apple-darwin10.8.0 (64-bit) locale: [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 attached base packages: [1] parallel stats graphics grDevices utils datasets methods [8] base other attached packages: [1] GEOquery_2.28.0 Biobase_2.21.7 BiocGenerics_0.7.5 [4] BiocInstaller_1.12.0 loaded via a namespace (and not attached): [1] RCurl_1.95-4.1 XML_3.95-0.2 On Mon, Mar 31, 2014 at 10:59 AM, BEN HAMDA Cherif <cherifbenhamda@gmail.com> wrote: > Hello, > I need help , > I have a problem with (GEOquery) package a > first of all, I can't download and this the warning message > > >library(GEOquery) > Setting options('download.file.method.GEOquery'='curl') > > > gds1257 <- getGEO('GDS858', destdir=".") > File stored at: > ./GDS1257.soft.gz > Error in read.table(con, sep = "\t", header = FALSE, nrows = nseries) : > invalid 'nlines' argument > > gds1257 > Error: object 'gds1257' not found > > The second problem is : > > If i download the gds file manually with "wget" and after that we use > the GDS2eSet i have this message : > > gds <- getGEO(filename='GDS1257.soft.gz') > eset <- GDS2eSet(gds, do.log2=TRUE) > File stored at: > /tmp/RtmpY4ZgWQ/GPL96.annot.gz > Error in read.table(con, sep = "\t", header = FALSE, nrows = nseries) : > invalid 'nlines' argument > > eset > Error: object 'eset' not found > > waiting response , thank you very much > > > Best > Cherif > > [[alternative HTML version deleted]] > > _______________________________________________ > 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]]