[BioC] two pair dye-swap (replicates) conducted in different labs

[Morten]

> 2) The result from IN HOUSE data seems to be nice, there are some DE 
> genes in the listing. Instead, there is nothing differencially 
> expressed genes for the data from OS LAB. So is it POSSIBLE? 
> Assuming it is possible 'cause variations  which came from operations 
> from different lab, what should I do from now on?

Hi.

Analyzing dye swap experiments in limma, yeld in my humble experience, very poor
satistics mainly due to gene specific dye bias. In addition when you have
relativily few arrays, you would expect to get poor statistics. 

One rather "ad hoc" method I use (and the statesticians probably dispise the
following. sorry:) 

x <- topTable(fit, adjust="fdr", sort.by="M", number=2000); y <- x[x$P.Value < 1
& (x$M > 0.5 | x$M < -0.5) & x$A > 9,];y; print("Number of genes in this
list:"); length(y$ID) #which gives you a toplist(y) of genes with M>|0.5| and
A>9 from the limma object "fit"

this I find usefull to analyse statisticly weak experiemnts (dye swap with few
arrays) to look for interesting genes.

hope this can be of any help
morten