hi, I am a newbie using this GEOquery package and have a couple of issues when I used it: 1. When I install it, there are two warnings, I think it could be specific to my Mac and should be ok. But I just want to confirm here. 2. When I used getGEO("GSE3210") then there is a kind of connection problem. I am wondering how to correct this? 3. When I download the gz file and run it locally, it seems working but ends with a couple of warnings (shown below). Is it ok? 4. BTW, it is really slow, even running from local. Should gunzipping at first help? The details of running can be seen from below. Thanks a lot! Weiwei > biocLite("GEOquery") Running getBioC version 0.1.8 with R version 2.3.1 Running biocinstall version 1.8.5 with R version 2.3.1 Your version of R requires version 1.8 of Bioconductor. trying URL 'http://bioconductor.org/packages/1.8/bioc/bin/macosx/i386/ contrib/2.3/GEOquery_1.7.2.tgz' Content type 'application/x-gzip' length 135676 bytes opened URL ================================================== downloaded 132Kb The downloaded packages are in /tmp/RtmpnbgyQZ/downloaded_packages Warning messages: 1: number of rows of result is not a multiple of vector length (arg 2) in: cbind(1, res0, Repository = repos) 2: cannot create HTML package index in: make.packages.html() > t0 <- getGEO("GSE3210") trying URL 'ftp://ftp.ncbi.nih.gov/pub/geo/data/geo/by_series/GSE3210/ GSE3210_family.soft.gz' Error in download.file(myurl, destfile, mode = mode) : cannot open URL 'ftp://ftp.ncbi.nih.gov/pub/geo/data/geo/by_series/GSE3210/GSE3210_fam ily.soft.gz' > t0 <- getGEO(filename="../data/GSE3210_family.soft.gz") Warning messages: 1: input string 1 is invalid in this locale in: grep.perl(pattern, x, ignore.case, value, useBytes) 2: input string 8592 is invalid in this locale in: grep.perl(pattern, x, ignore.case, value, useBytes) 3: input string 8592 is invalid in this locale in: grep.perl(pattern, x, ignore.case, value, useBytes) 4: input string 8592 is invalid in this locale in: grep.perl(pattern, x, ignore.case, value, useBytes) 5: input string 8592 is invalid in this locale in: grep.perl(pattern, x, ignore.case, value, useBytes) 6: input string 8592 is invalid in this locale in: grep(pattern, x, ignore.case, extended, value, fixed, useBytes) -- Weiwei Shi, Ph.D Research Scientist GeneGO, Inc. "Did you always know?" "No, I did not. But I believed..." ---Matrix III

On Friday 03 November 2006 13:17, Weiwei Shi wrote: > hi, > > I am a newbie using this GEOquery package and have a couple of issues > when I used it: > 2. When I used > getGEO("GSE3210") > then there is a kind of connection problem. I am wondering how to correct > this? You will need to use the version from 1.9 or 2.0 (devel) of Bioconductor. The URL for GEO changes relatively regularly, which is what causes this problem. > 3. When I download the gz file and run it locally, > it seems working but ends with a couple of warnings (shown below). Is it > ok? This has to do with the encoding in the file being incorrect. This isn't SUPPOSED to happen, but I have seen this also. You may have to do some simple checks to make sure that you have all the samples represented, etc. > 4. BTW, it is really slow, even running from local. Should gunzipping > at first help? I'm not sure what you mean by slow, but it is parsing a 4.7 million line file, so that may take a while. Gunzipping will not help significantly-- sorry. Sean