[BioC] GEOquery: how to extract experimental data? (confused)
Freudenberg, Johannes (NIH/NIEHS) [E]
johannes.freudenberg at nih.gov
Thu Aug 18 15:18:23 CEST 2011
Your R code worked fine for me. Not sure what the issue is. One work-around would be to
1. manually download the Series Matrix file (ftp://ftp.ncbi.nih.gov/pub/geo/DATA/SeriesMatrix/GSE19044/GSE19044_series_matrix.txt.gz) into your working directory
2. slightly modify your R code:
> u = getGEO(file="GSE19044_series_matrix.txt.gz")
From: Dai, Hongying, [mailto:hdai at cmh.edu]
Sent: Wednesday, August 17, 2011 2:51 PM
To: 'bioconductor at r-project.org'
Subject: Re: [BioC] GEOquery: how to extract experimental data? (confused)
Hi, Jose and Sean
I try to run the exactly same code as you guys provided to extract GS19044 data. But I failed with connection issue. Here is my code and system information:
R> source("http://www.bioconductor.org/biocLite.R") # It connected to
R> the cite successfully
BioC_mirror = http://bioconductor.org
Change using chooseBioCmirror().
1: In safeSource() : Redefining 'biocinstall'
2: In safeSource() : Redefining 'biocinstallPkgGroups'
3: In safeSource() : Redefining 'biocinstallRepos'
library(Biobase) # no error message
library(GEOquery) # no error message
R> u = getGEO('GSE19044')
Error in curlPerform(curl = curl, .opts = opts, .encoding = .encoding) :
couldn't connect to host
R version 2.13.1 (2011-07-08)
Platform: i386-pc-mingw32/i386 (32-bit)
 LC_COLLATE=English_United States.1252  LC_CTYPE=English_United States.1252  LC_MONETARY=English_United States.1252  LC_NUMERIC=C  LC_TIME=English_United States.1252
attached base packages:
 tools stats graphics grDevices utils datasets methods
other attached packages:
 ff_2.2-3 bit_1.1-7 GEOquery_2.19.2 Biobase_2.12.2
loaded via a namespace (and not attached):
 RCurl_1.6-7.1 XML_3.4-2.2
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