[BioC] No replicates and differential analysis !!

Ben Bolstad bmb at bmbolstad.com
Wed Jan 25 16:54:44 CET 2006

While I agree wholeheartedly with what others state on the issue of
replication and external validation (eg PCR) you might be able to do
slightly better with a test statistic based on a probe level analysis.
Admittedly there is no polished function for doing this in general right
now, but something like

my.abatch <- ReadAffy()
my.Pset <- fitPLM(my.abatch)

##now assuming you have only two samples

PLM.teststatistic <- (coefs(my.Pset)[,1] -
coefs(my.Pset)[,2])/(sqrt(se(my.Pset)[,1]^2 + se(Pset)[,2]^2)

I have observed that you do slightly better thresholding on this than FC
(or log FC to be more exact) on spike-in datasets.

Hope that helps,


On Wed, 2006-01-25 at 14:34 +0100, Nicolas Servant wrote:
> Hello,
> Does anybody know a R package or function to compare expression level 
> (affy data) of two groups with no replicates in each group ? In fact, 
> just compare one array to an other.
> The purpose is to find differentially expressed genes.
> We cannot used statistical test (not enougth replicates), but we can 
> used graphical approach based on scatter plot, and outliers detection 
> approach.
> Thanks for your help,
> Regards
> Nicolas.

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