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

[Massimo Pinto]

Hello John

On Wed, Jun 10, 2009 at 12:15 PM, john seers
(IFR)<john.seers at bbsrc.ac.uk> wrote:
>
> 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.
>

I have played around with topTable() and topTableF() and I am getting
to knowing it better now. However, I am missing the point you are
making here above. I cannot see how do you pass topTable() info with
regards to which genes or which set of genes you wish to know about.

I am assuming that topTable() was designed for this purpose, but since
this is coming towards interrogating user-specified sets of genes, I
may be wrong.

Cheers
Massimo