[BioC] PreProcess and Limma 'done'. What directions now?

[john seers (IFR)]

Hi Massimo

>I have beem through normalization and basic limma operations. 

Does this mean you have extracted lists of genes using topTable? You can
add your annotation to these lists of genes using the "genelist"
parameter of topTable. Something like "genelist=cbind(fit$genes,
mappings)". Assuming your mappings are in the same order as your fit
data.

>What I would like to do here is to ask questions like "what happened to
this
>and that particular gene"? 

You can extract any gene you like from a topTable gene list. Along with
the expression/p-values etc. You can extract the actual expression
values using the Affymetrix probe name or your gene annotation name.


> in place of their Agilent Probe ID. Should be
> possible, since I have an annotation file.

Yes.

Regards

John