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

[john seers (IFR)]

Hi Massimo

You are probably reading too much into what I said. I was just trying to
say to you that you can combine your annotation information with the
Affymetrix probes and the limma output. And Vincent gave you information
on how you can search the annotation data.

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

Without this question being more definite it is not easy to predict what
you need to do. What I was saying is you can search on your expression
values by Affymetrix probe (or Annotation id), or on your toptables, to
extract any gene or genes of interest. That defines what has happened to
this and that particular gene. What you want to do further is an open
question. 

Are you asking how to search for a gene in a toptable? Something like:

geneofinterest<-"myaffymetrixprobe"
myrows<-which(mytoptable[, "correctcolumnname"] == geneofinterest)
mygeneofinterest<-mytoptable[myrows,]


Sorry if I do not understand what you need to know.

Regards

John




-----Original Message-----
From: Massimo Pinto [mailto:pintarello at gmail.com] 
Sent: 11 June 2009 11:29
To: john seers (IFR)
Cc: bioconductor at stat.math.ethz.ch
Subject: Re: [BioC] PreProcess and Limma 'done'. What directions now?

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