DESeq2

[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It looks like you have a mix of out-of-date and new packages.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