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

[Adaikalavan Ramasamy]

Besides being ad-hoc, the codes are almost unreadable.

Why you have chosen the cutpoints of 0.5 and 9 ?

Regards, Adai


On Tue, 2005-09-20 at 10:54 +0200, Morten wrote:
> > 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
> 
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