Question: Deseq - Problem With Plotma Function
0
gravatar for Biomonika (Noolean)
6.1 years ago by
State College, PA, USA
Biomonika (Noolean)3.0k wrote:

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 :-)

deseq plot • 2.5k views
ADD COMMENTlink modified 6.0 years ago • written 6.1 years ago by Biomonika (Noolean)3.0k

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.

ADD REPLYlink written 6.1 years ago by Biomonika (Noolean)3.0k
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