comparison limma_voom.R @ 16:5d903d528193 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 349e35a66009449851b21e2810bc5aaa58225fca

15:41573afd6871

    downCount[i] <- sumStatus["Down", i]
    flatCount[i] <- sumStatus["NotSig", i]

    # Write top expressions table
    if (wantTreat) {
        top <- topTreat(fit, coef=i, number=Inf, sort.by="P")
    } else{
        top <- topTable(fit, coef=i, number=Inf, sort.by="P")
    }
    write.table(top, file=topOut[i], row.names=FALSE, sep="\t", quote=FALSE)
    linkName <- paste0(deMethod, "_", con, ".tsv")
    linkAddr <- paste0(deMethod, "_", con, ".tsv")
    linkData <- rbind(linkData, c(linkName, linkAddr))

16:5d903d528193

    downCount[i] <- sumStatus["Down", i]
    flatCount[i] <- sumStatus["NotSig", i]

    # Write top expressions table
    if (wantTreat) {
        top <- topTreat(fit, coef=i, adjust.method=opt$pAdjOpt, number=Inf, sort.by="P")
    } else{
        top <- topTable(fit, coef=i, adjust.method=opt$pAdjOpt, number=Inf, sort.by="P")
    }
    write.table(top, file=topOut[i], row.names=FALSE, sep="\t", quote=FALSE)
    linkName <- paste0(deMethod, "_", con, ".tsv")
    linkAddr <- paste0(deMethod, "_", con, ".tsv")
    linkData <- rbind(linkData, c(linkName, linkAddr))