DESeq2 colData pData

[coutellec]

Dear all,

In the vignette of DESeq2, the example given for DESeqDataFromMatrix is based on the pasilla dataset. I cannot apply function "pData" when trying to build the colData dataframe.
Can you help?
thanks in advance
Agnès

[Michael Love]

It sounds like you skipped one of the steps loading libraries, in particular:

library("Biobase")

[albireo]

I had the same problem. Would the author of the package be so kind to update the vignette to specify that the package Biobase is required? Thanks a lot!

[Michael Love]

I don't understand the confusion.

library("Biobase")

is the first line of the chunk for section 1.2.3 "Count matrix input" in the vignette on page 4.

Note that pData is only needed in the case that you are importing RNA-Seq count data from a DESeq::CountDataSet or an ExpressionSet.

[albireo]

I was going through a hardcopy version of the vignette and the line you mention is not there. It might have been added afterwards. Thanks for the help!