[BioC] SAM timecourse or what else ?

[Ana Conesa]

Hi Davide

You could use the maSigPro package for this. Time is treated
quantitatively and with a little modification in the default created
design, you can find those genes whith an homogeneous pattern across
patients considering some intra-patient dependency. I am enclosing
you a little script on how to proceed in this case, taken either a
quadratic and cubic regression model.

Hope this helps

Ana

-------------------------------------------
Ana Conesa, PhD
Bioinformatics Department
Centro de Investigación Príncipe Felipe
Avda. Autopista Saler 16
46013 Valencia Spain
http://bioinfo.cipf.es
===========================================
CAMDA2007 Conference @ CIPF
http://camda.bioinfo.cipf.es
===========================================


>
>
>---- Mensaje Original ----
>De: Davide.Valentini at ki.se
>Para: bioconductor at stat.math.ethz.ch
>Asunto: RE: [BioC] SAM timecourse or what else ?
>Fecha: Thu, 09 Aug 2007 10:44:33 +0200
>
>>
>>
>>Hi to all,
>>
>>I have a dataset of 5 patients each one taken in 4 different times
>>
>>gene    P1-T1    P1-T2    P1-T3    P1-T4    P2-T1    P2-T2    ...
>>
>>AAA    42    22    232    ...    ...    ...    ...
>>BBB    33    76    200    ...    ...    ...    ...
>>CCC    123    22    11    ...    ...    ...    ...
>>...    ...
>>
>>I'm mostly interested to the evaluate the change in gene expression
>over 
>>time, for this I was thinking to use the "quantitative" option in
>samr 
>>package, but I'm also curious about "One class timecourse" (I know
>that 
>>is not in BioC but maybe someone already used it). I don't find any 
>>examples in the documentation, and I don't know IF and how to
>proceed. 
>>Any help ? :)
>>Secondly I'm also interested to group the patients with the same
>trends.
>>So my question also is: Do you have some suggestions about what 
>>technique (or packages) to use for BOTH this tasks ?
>>
>>Thanks in advance to all, and sorry if part of the question is not 
>>strictly regarding BioConductor.
>>Regards
>>
>>Davide
>>
>>
>>-- 
>>Davide Valentini
>>Postdoc - Biostatistician
>>Department of Medical Epidemiology and Biostatistic
>>Karolinska Institute
>>Box 281
>>SE-171 77 Stockholm
>>SWEDEN
>>Tel: +46-8-524 82294
>>Fax: +46-8-31  4975
>>
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>ormatics.conductor
>>

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