Problem with GDS2eSet
1
0
Entering edit mode
@cherif-ben-hamda-6478
Last seen 6.0 years ago
Tunisia
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]]
• 1.2k views
ADD COMMENT
0
Entering edit mode
@sean-davis-490
Last seen 12 weeks ago
United States
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 I suspect that you are using an outdated version and need to upgrade.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]]
ADD COMMENT

Login before adding your answer.

Traffic: 1034 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6