[BioC] RE: Bioconductor digest, Vol 1 #210 - 10 msgs

[Jeff Sorenson]

Can anyone point me to a reference where these numbers regarding false
positives were derived?  This is a huge difference!

Thanks,

Jeff Sorenson
>
> two things to keep in mind:
>
> 1) rma return log2 expression so make
> sure to use 2^(exp1-exp2) to compute fold change.
>
> 2) rma sacrifices a bit in bias for big gains in precission. for example,
> using affymetrix's spike in data and using the fold-change>2 criteria
> (ignoring presence absent calls) to define differentially expressed genes,
>
>     MAS 5.0 gives you, on average, 12.5 true positives (out of 14 truely
>     differentially expressed genes) but 3110 false positives.
>
>     RMA on the other hand gives you a bit smaller average # of true
>     positives, 11.6, but a much smaller average # of false positives: 18.
>
> hope this helps,
> rafael
>
>