[BioC] To get expression data from GEO

[vegardny]

Hi Jerry.

The GSE27597 data set seems to consist of data from two different array 
platforms, so getGEO returns a list of two ExpressionSet objects. You 
need to use the list accessor, [[]], to get the individual elements.

Something like this:

library(GEOquery)
data1 = getGEO("GSE27597")
datExpr1 = exprs (data1[[1]])
dim(datExpr1) # the first smaller data set
datExpr2 = exprs (data1[[2]])
dim(datExpr2) # the second larger


And your line
datExpr = exprs (data1)
Just gave an error for me, so You might be using an old version of 
GEOquery.

This is my
sessionInfo()
R version 3.0.2 (2013-09-25)
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 
  base

other attached packages:
[1] GEOquery_2.28.0    Biobase_2.22.0     BiocGenerics_0.8.0

loaded via a namespace (and not attached):
[1] RCurl_1.95-4.1 XML_3.95-0.2

Vegard.


On 2014-03-25 23:47, Jerry Cholo wrote:
> Hello,
> 
> 
> I would like to have expression data for GSE27597.  When I ran 
> following
> command line:
> 
> 
> 
> data1 = getGEO("GSE27597")
> 
> 
> 
> I noticed that there are two files related to this GSE (see below):
> 
> 
> 
> 
> 
> Found 2 file(s)
> 
> 
> GSE27597-GPL13243_series_matrix.txt.gz
> 
> Using locally cached version:
> C:\Users\AppData\Local\Temp\RtmpodgO6C/GSE27597-GPL13243_series_matrix.txt.gz
> 
> Using locally cached version of GPL13243 found here:
> 
> C:\Users\AppData\Local\Temp\RtmpodgO6C/GPL13243.soft
> 
> 
> 
> GSE27597-GPL5175_series_matrix.txt.gz
> 
> Using locally cached version:
> C:\Users\AppData\Local\Temp\RtmpodgO6C/GSE27597-GPL5175_series_matrix.txt.gz
> 
> Using locally cached version of GPL5175 found here:
> 
> C:\Users\AppData\Local\Temp\RtmpodgO6C/GPL5175.soft
> 
> 
> 
> When I ran following line
> 
> 
> 
>  datExpr = exprs (data1)
> 
> 
> 
> to get expression data I did not get the main data that includes more
> samples, but I got the smaller dataset that has few samples.
> 
> 
> 
> May someone let me know how I could deal with this problem?
> 
> 
> 
> Thanks,
> 
> Jerry
> 
> 	[[alternative HTML version deleted]]
> 
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