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

J.delasHeras at ed.ac.uk J.delasHeras at ed.ac.uk
Tue Aug 16 14:31:57 CEST 2011

Quoting Vincent Carey <stvjc at channing.harvard.edu> on Tue, 16 Aug 2011  
07:38:19 -0400:

> you have noted that getGEO returns a list, and the first element of the list
> you got is an ExpressionSet instance.
> you are asking about access to the assayData.  This concerns ExpressionSet
> mechanics, not GEOquery
>> library(Biobase)
> Welcome to Bioconductor
>   Vignettes contain introductory material. To view, type
>   'browseVignettes()'. To cite Bioconductor, see
>   'citation("Biobase")' and for packages 'citation("pkgname")'.
>> data(sample.ExpressionSet)
>> assayData(sample.ExpressionSet)
> <environment: 0x100b1eb40>
>> ls(.Last.value)
> [1] "exprs"    "se.exprs"
>> dim(assayData(sample.ExpressionSet)$exprs)
> [1] 500  26
>> dim(assayData(sample.ExpressionSet)$se.exprs)
> [1] 500  26
>> dim(exprs(sample.ExpressionSet))
> [1] 500  26
> assayData is not intended for direct handling by end users.  the exprs()
> method will retrieve the matrix of expression
> values.

Hi Vincent,

thanks for that, I'll use the methods for the ExpressionSet class, but  
it was interesting to see how to look at the contents of the assayData  
teh way you did. I'm used to typing 'ls()', without arguments, to  
check teh contents of my current workspace, and didn't think of  
checking what arguments I could specify.


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