[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

Hi Daisy,

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: 

> library(GEOquery)
> u = getGEO(file="GSE19044_series_matrix.txt.gz")
> head(exprs(u))


-----Original Message-----
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().
Warning messages:
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> sessionInfo()
R version 2.13.1 (2011-07-08)
Platform: i386-pc-mingw32/i386 (32-bit)

[1] LC_COLLATE=English_United States.1252 [2] LC_CTYPE=English_United States.1252 [3] LC_MONETARY=English_United States.1252 [4] LC_NUMERIC=C [5] LC_TIME=English_United States.1252

attached base packages:
[1] tools     stats     graphics  grDevices utils     datasets  methods
[8] base

other attached packages:
[1] ff_2.2-3        bit_1.1-7       GEOquery_2.19.2 Biobase_2.12.2

loaded via a namespace (and not attached):
[1] RCurl_1.6-7.1 XML_3.4-2.2


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