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

[Massimo Pinto]

John,

you ended up getting very close to were I needed to be. To compare
microarray results to previous data which I had got using other
techniques to measure gene expression, I was asked by a colleague to
report the micraorray expression levels of selected genes of our
interest.

much inspired by what you did, I proceed as follows:

First I created a vector of probeID:

> GOI.redox # vector of genes of interest in the context: redox
[1] "A_23_P150281" "A_24_P89457"  "A_23_P3038"   "A_23_P133474"
"A_23_P28075"  "A_23_P214544" "A_23_P250671" "A_32_P78121"
"A_23_P154840" # "A_23_P105138"

then, for a given topTable such as

> t0Cn.Vs.6moACn.topTable <- topTable(fit2.Cn.eb, coef=1, genelist=cbind(mappings$DESCRIPTION, fit2.Cn.eb$genes), number=Inf, adjust="BH")

I defined a loop to find where all those probes are in the topTable

>for (i in 0:length(GOI.redox)) {
+ myrows[i] <- which(t0Cn.Vs.6moACn.topTable[, "ID"] == GOI.redox[i])
+ }

> t0Cn.Vs.6moACn.topTable[myrows,]  # outputs a specified portion of your topTable with the genes that you wanted.

that does it. May be not the most elegant syntax, as I suppose one may
well do without a loop, but it does just what I need to show my
colleague.

Cheers, once again!
Massimo



On Thu, Jun 11, 2009 at 1:02 PM, john seers (IFR)<john.seers at bbsrc.ac.uk> wrote:
>
> 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
>



-- 
Massimo Pinto
Post Doctoral Research Fellow
Enrico Fermi Centre and Italian Public Health Research Institute (ISS), Rome
http://claimid.com/massimopinto