I am now getting familiar with DESeq :-)
I tried following code with passilla data from DESeq vignette:
pasillaCountTable = read.table("passillaData", header=TRUE, row.names=1 ) pasillaDesign = data.frame( row.names = colnames( pasillaCountTable ), condition = c( "untreated", "untreated", "untreated", "untreated", "treated", "treated", "treated" ), libType = c( "single-end", "single-end", "paired-end", "paired-end", "single-end", "paired-end", "paired-end" ) ) pasillaDesign pairedSamples = pasillaDesign$libType == "paired-end" countTable = pasillaCountTable[ , pairedSamples ] condition = pasillaDesign$condition[ pairedSamples ] head(countTable) condition library( "DESeq" ) cds = newCountDataSet( countTable, condition ) cds = estimateSizeFactors( cds ) sizeFactors( cds ) head( counts( cds, normalized=TRUE ) ) cds = estimateDispersions( cds ) str( fitInfo(cds) ) res = nbinomTest( cds, "untreated", "treated" ) head(res) plotMA(res) #hist(res$pval, breaks=100, col="skyblue", border="slateblue", main="")
I use environment of RStudio. Histogram si visualised without any problem, however plotMA yields in following error:
> plotMA(res) Error in MA[, array] - x : non-numeric argument to binary operator In addition: There were 50 or more warnings (use warnings() to see the first 50)
I believe that I used sample data and commands from the package. Has anybody encountered the same problem? :-)
Or does anyone happen to have the smallest working example of DESeq script?
EDIT: I decided to use DESeq2 instead. So far it seems like a solution to my DESeq problems :-)