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

[Massimo Pinto]

Hi Steve and all,

On Tue, Jun 9, 2009 at 5:15 PM, Steve
Lianoglou<mailinglist.honeypot at gmail.com> wrote:
> Hi Massimo,
>
> On Jun 9, 2009, at 9:13 AM, Massimo Pinto wrote:
>
>> Greetings BioC list readers,
>>
>> I have been working over the past few weeks on data normalization
>> first (Agi4X44PreProcess) and linear models then (limma). I sense that
>> I may have reached a point where questions may be addressed regarding
>> regulation of individual genes of interest, as well as gene ontology.
>>
>> Would you please so kindly provide advice with regards to my next
>> step? In brief, I would like to
>>
>> 1) Query expression of genes of my interest, which are known to be
>> implicated in the biology that I am working on
>
> I'm not sure what you're asking to do here, actually, since after doing your
> normalization/etc. this is the easy part, right?
>
> You can just select these rows out of your normalized data matrix, or
> highlight their probe values on an MA plot, or plot their points on a pdf of
> your signal intensities. If you're looking for their differential expression
> calls, you'd just extract their +1/-1 calls post-limma-facto, if you will
> :-)

I have beem through normalization and basic limma operations. What I
would like to do here is to ask questions like "what happened to this
and that particular gene"? These would be genes whose expression was
already measured via other techiniques (Rt-PCR as well as Western
Blotting of the proteins that they encode). Ideally, I would like to
produce a mini-list of such genes and have their Gene ID displayed (in
tables and any graphs) in place of their Agilent Probe ID. Should be
possible, since I have an annotation file.

> mappings[1:10,1:4]

          PROBE    ACCNUM       SYMBOL  ENTREZID
1   A_24_P66027 NM_004900     APOBEC3B      9582
2   A_32_P77178  AA085955         ADAR       103
3  A_23_P212522 NM_014616       ATP11B     23200
4  A_24_P934473  AK092846 LOC100132006 100132006
5    A_24_P9671 NM_001539       DNAJA1      3301
6  A_24_P801451 NM_006709        EHMT2     10919
7   A_32_P30710 NM_000978        RPL23      9349
8  A_24_P704878        NA           NA        NA
9   A_32_P86028 NM_001017        RPS13      6207
10  A_23_P65830 NM_198527        HDDC3    374659


>> 2) Get information about gene ontology
>
> There are several package you can check. You've already mentioned
> goProfiles, but you might also want to consider GOstats as well. There's
> also topGO.

thank you.

>
>> 3) Ask about involvement of signaling pahways
>
> I'm not sure about this one, but searching the bioconductor d/l page for the
> word "pathway" comes up with several leads, like SPIA and sigPathway.
>
> I've never used either of these, but perhaps you can let us know how you
> like them :-)

Will do!
Thank you.
Massimo


> --
> Steve Lianoglou
> Graduate Student: Physiology, Biophysics and Systems Biology
> Weill Medical College of Cornell University
>
> http://cbio.mskcc.org/~lianos
>
>
>
>



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