<melissa.martin at="" ...=""> writes: > > I am trying to use the DEseq package without replicates. When I look for significant hits all of them are > False. Could this be a real result? Below are the commands that I enter. > > > countsTable <- read.delim("spore_readcounts.txt",header=TRUE,stringsAsFactors=TRUE) > > rownames( countsTable ) <- countsTable$gene_id > > countsTable <- countsTable[ , -1 ] > > head(countsTable) > > cds <- newCountDataSet( countsTable, conds ) > > cds <- estimateSizeFactors( cds ) > > sizeFactors( cds ) > > head( counts( cds, normalized=TRUE ) ) > > cds <- cds[ ,c( "1", "2" ) ] > > cds <- estimateDispersions( cds, method="blind", sharingMode="fit- only" ) > > res <- nbinomTest( cds, "1", "2" ) > > plotDE( res ) > Error: could not find function "plotDE" > > addmargins( table( res_sig = res$padj < .1, res_sig = res$padj < .1 ) ) > res_sig > res_sig FALSE Sum > FALSE 4960 4960 > Sum 4960 4960 > > Many Thanks > > Melissa > > > > _______________________________________________ > Bioconductor mailing list > Bioconductor at ... > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor Hi Melissa, As far as I have noticed, you forgot to write the code for plotDE(). plotDE <- function( res ) plot( res$baseMean, res$log2FoldChange, log="x", pch=20, cex=.1, col = ifelse( res$padj < .1, "red", "black" ) ) plotDE( res ) Now, I think it should run... All the best! Aso