[BioC] Analysis for only 2 replicates

[Xuejun Liu]

There is an R package called 'pplr' which makes use of probe-level
variance within chips. It handles small number of chips quite well. It
might help. You can find it from
http://umber.sbs.man.ac.uk/resources/puma/index.html.

Cheers,
Xuejun

On Thu, 2006-03-09 at 00:34, fhong at salk.edu wrote:
> Based on my experience,SAM usually fails with only 2 replicates under each
> condition.
> Limma and RankProd both can handle 2 replicates.
> 
> Fangxin
> 
> >
> >
> >
> > On 3/8/06 4:07 PM, "Khan, Sohail" <khan at cshl.edu> wrote:
> >
> >> Dear list,
> >>
> >> I have 2 -wt and 2-mutant samples done on Affymetrix chips.
> >> Could you suggest the best way to analyze this experiment? Is averaging
> >> both
> >> replicates and picking genes based on fold change good??
> >> Thanks for any suggestions.
> >
> > I wouldn't average if you can help it (if these are biological
> > replictes--if
> > they are not, then I would argue that you don't actually have any
> > replication).  You are then very much at the mercy of the outliers.  I
> > would
> > try using limma or SAM, or one of several other methods for looking at
> > microarray data designed with small samples in mind.
> >
> > That said, any results that you find are very suspect with only two
> > replicates per condition, but if you are only interested in finding
> > candidates for further analysis (the best you can hope to do with only
> > four
> > arrays), the ordering you get would, I think, be more robust using a
> > statistical test than simple averaging.
> >
> > Sean
> >
> > _______________________________________________
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> >
> >
> 
> 
> --------------------
> Fangxin Hong  Ph.D.
> Plant Biology Laboratory
> The Salk Institute
> 10010 N. Torrey Pines Rd.
> La Jolla, CA 92037
> E-mail: fhong at salk.edu
> (Phone): 858-453-4100 ext 1105
> 
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