[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
>
> NULL 

Hi,

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.

Regards,
Joern



More information about the Bioconductor mailing list