Question: LIMMA:nestedF
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13.5 years ago by
Hi, I have a question about decideTests with method "nestedF". As I saw, this function can't handle with NA values! How can I realize a nestedF classification with a fit with NA values? I found two solutions by myself. But I'm not sure about!!! 1) I've tryed to list the function decideTests and then I've created a new function decide.mine only -removing if anyis.na(object$F.p.value))) stop("nestedF method can't handle NA p-values", call. = FALSE) from the code -and rewriting sel <- p.adjust(object$F.p.value, method = adjust.method) < p.value sel<-(!is.na(sel)) I've tryed also with: fit<-lmFit(MA,design,ndups=1) fit2<-contrasts.fit(fit,cont.matrix) fit2<-eBayes(fit2) fit2$F.p.value<-p.adjust(fit2$F.p.value, method = "HY") results<-classifyTestsF(fit2,p.value=0.001) which one is correct? Or otherwise How I can manage, to apply nestedF approach with an MA-list with NA values?? Thanks in advance Daniela
classification • 577 views