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

[Joern Toedling]

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