[BioC] DESeq without replicates, Problem trying to obtain significant hits

[Asma]

 <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
> 
> 
> 
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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