[BioC] Analysis for only 2 replicates

[Sean Davis]

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