

Hi, sorry for the stupid question, I'm quite a beginner and I'm not totally sure about what I'm doing...and this is not good.

I used limma library, fitted with lmFit, then fitted some contrasts (three), then Differential expression with eBayes.
Until here everything is fine, 100% sure.

for diagnostic purposes I want to have a plot of t values vs log(stdDev).
I used slot "t", to extract the t values (I'm interested only in the second contrast among the ones I computed)

>x<- fitted$t[,2]

And slot "s2.post" to extract the variance, and to compute the logged st. dev.

>y<-log2(sqrt(fitted$s2.post))

so I can plot using

>require(geneplotter)
>smoothScatter(x, y)

Am I doing right ?

Thanks,

G







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