search for: diffgenes

...frame into a new data frame based on selection criteria. What I've done is this: all.comps <- ls(pattern="^res") for(i in all.comps){ obj = i; gene.ids = rownames(obj$counts); x = data.frame(gene.ids = gene.ids, obj$counts, obj$e1, obj$e2, obj$log.fc, obj$p.value, obj$q.value); DiffGenes.i = subset(x, x$obj.p.value<0.05 | x$obj.q.value<=0.1) } Obviously, this doesn't work because pattern searching in the first line is not feeding the entire data structure into the all.comps variable. But how can I accomplish feeding the whole data structure for each one of these lists in...

...]]; >> + gene.ids = rownames(obj$counts); >> + x = data.frame(gene.ids = gene.ids, obj$e1, obj$e2, obj$log.fc, >> + obj$p.value, obj$q.value); x = subset(x, x$obj.p.value<0.05 | >> + x$obj.q.value<=0.1); cat("output object name is: >> + ",paste("Diffgenes",i,sep="."),"\n"); >> + cat("output object data is: \n"); >> + print(tmp); >> + cat("\n"); >> + } >> Error in all.comps[[i]] : subscript out of bounds >> >> >> In response to another helpful suggestion, her...