[BioC] GEOquery: how to extract experimental data? (confused)

J.delasHeras at ed.ac.uk J.delasHeras at ed.ac.uk
Tue Aug 16 13:20:29 CEST 2011

I have been until now downloading GEO data directly to my computer and  
using basic R functions to load tables and process them.
It works, but I figured I would probably save time if I learn to use  
the GEOquery package, which looks promising.

However, I'm failing tremendously at my first attempt. I can get a lot  
of good information, except the actual experiment data... and it seems  
to be there, but can't get to it!

Example. I'm trying to get GSE19044, which contains 42 samples and  
uses the Illumina WG6 platform, which is great as I'm familiar with it.

so I do:

u = getGEO('GSE19044')

> show(u)
ExpressionSet (storageMode: lockedEnvironment)
assayData: 45281 features, 42 samples
   element names: exprs
protocolData: none
   sampleNames: GSM471318, GSM471319, ..., GSM471359  (42 total)
   varLabels and varMetadata description:
     title: NA
     geo_accession: NA
     ...: ...
     data_row_count: NA
     (39 total)
   featureNames: ILMN_1212602, ILMN_1212603, ..., ILMN_3163582  (45281 total)
   fvarLabels and fvarMetadata description:
     ID: NA
     Species: NA
     ...: ...
     SPOT_ID: NA
     (31 total)
   additional fvarMetadata: Column, Description
experimentData: use 'experimentData(object)'
Annotation: GPL6887

It looks good. It looks like what I want is the 'assayData'. But I  
can't get to it.

'u' is a list, containing one element...
> class(u)
[1] "list"
> length(u)
[1] 1

> class(u[[1]])
[1] "ExpressionSet"
[1] "Biobase"

ok, so I rename that, and look at its structure:


> str(eset)
Formal class 'ExpressionSet' [package "Biobase"] with 7 slots
   ..@ assayData        :<environment: 0x0645ec5c>
   ..@ phenoData        :Formal class 'AnnotatedDataFrame' [package  
"Biobase"] [...] (omitted for brevity)

I can extract the sample names, the basic annotation/probe identity  
etc easily:
eset at phenoData@data #samples
eset at featureData@data #annotation

but how do I get into 'assayData'?
from the 'show(u)' it looks like it contains what I am after: 45281  
features, 42 samples ... but it's class 'environment' and that's  
throwing me off.

I was looking into the GEOquery user guide, but I'm still none the wiser.

How do I get in there?

thanks for any help.


Dr. Jose I. de las Heras                      Email: J.delasHeras at ed.ac.uk
The Wellcome Trust Centre for Cell Biology    Phone: +44 (0)131 6507090
Institute for Cell & Molecular Biology        Fax:   +44 (0)131 6507360
Swann Building, Mayfield Road
University of Edinburgh
Edinburgh EH9 3JR

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Scotland, with registration number SC005336.

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