[Bioc-devel] GEOquery function getGEO broken?

Valerie Obenchain vobencha at fhcrc.org
Wed Sep 14 18:07:41 CEST 2011

Hi Andreas,

I'm not able to reproduce your problem. After updating your packages 
with biocLite, does this simple example work for you,

gds858<- getGEO('GDS858')  #GSEMatrix=TRUE is default

If possible, please provide some code that reproduces your problem and the output of your sessionInfo().


my sessionInfo() on R-2.13,

>  sessionInfo()
R version 2.13.0 Patched (2011-04-19 r55540)
Platform: x86_64-unknown-linux-gnu (64-bit)

[1] C

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

other attached packages:
[1] GEOquery_2.19.4 Biobase_2.12.1

loaded via a namespace (and not attached):
[1] RCurl_1.5-0  XML_3.2-0    tools_2.13.0

On 09/06/11 08:07, Andreas Heider wrote:
> Dear mailing list,
> when using the GEOquery function getGEO(GSExyz, GSEMatrix=T). I get an
> error, that featureNames and rownames in exprs slot are different.
> What would have caused this error? I used this function in version 2.18.0
> and in version 2.19 it doesn't work anymore.
> Thanks, Andreas
> PS: I'm running R 2.13.0 with GEOquery 2.18 and R 2.13.1 with GEOquery 2.19
> 	[[alternative HTML version deleted]]
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