[Caitriona McEvoy]

Hi all,
I am very new to r & DEseq2 but have been following the excellent vignette. I have encountered a problem though. I can create the object rld as per the command in the vignette, but when I try to run PCA as suggested I repeatedly encounter the following error:

plotPCA(rld, intgroup=c("Fibrosis", "Sample.ID"))

Error in (function (classes, fdef, mtable) :
unable to find an inherited method for function ‘plotPCA’ for signature ‘"SummarizedExperiment"’
I have also tried:
plotPCA( DESeqTransform(rld ) )
and get the following:
Error in plotPCA(DESeqTransform(rld)) :
error in evaluating the argument 'x' in selecting a method for function 'plotPCA': Error: could not find function "DESeqTransform"
Can anyone advise?
Caitriona

[dpryan]

How did you make "rld" and what version of DESeq2 are you using?

[Caitriona McEvoy]

Thanks for replying. I am using DESeq2 1.6.3.
First I made dds:
dds <- DESeqDataSetFromMatrix(countData = countData,
colData = colData,
design = ~ Organ + Fibrosis)
then:
rld = rlog (dds)
I went on to examine rld using: head(assay(rld)), and it is listed in my environment as a large SummarisedExperiment.
Caitriona

[Michael Love]

hi Caitriona

It looks like you have a mix of out-of-date and new packages. These often generate conflicts. This can occur if you install Bioconductor packages using install.packages() rather than with biocLite().

Try this:

source("http://bioconductor.org/biocLite.R")
biocValid()

[Caitriona McEvoy]

Hi Michael, Thank you for your reply. I installed packages as suggested, and it's working. Thanks! Caitriona