[BioC] how to get the normalized genes expression values with vsn

Joern Toedling toedling at ebi.ac.uk
Wed Jun 1 10:18:22 CEST 2005

diego huck wrote:

> Hello
> I normalized a data.frame with genes in rows and conditions in columns 
> with vsn
> genormalized <- vsn(ge)
> latter I tried to get the normalized values with the following command 
> but I didn't get the result I need
> genormalized$exprs


you use the dollar sign to get list components, but the expression
matrix is a slot of the exprSet and thus can be accessed by
'genormalized at exprs' or  'exprs(genormalized)' (have a look at
help(exprSet) to learn about other methods). The result can be written
by 'write.table', but most Bioconductor functions are able to handle
'exprSet' objects.


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