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 _________________________________________________________________ Le più cercate della settimana? [[alternative HTML version deleted]]