Entering edit mode
11.0 years ago
Biomonika (Noolean)
3.2k
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 :-)
i would like to add that when I use sample code of plotMA from limma package I do get a nice graph. So the problem is probably with my values in res variable.