Announcement

Collapse
No announcement yet.

DESeq2

Collapse
X
 
  • Filter
  • Time
  • Show
Clear All
new posts

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

    Comment


    • 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

      Comment


      • 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        It looks like you have a mix of out-of-date and new packages.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()

        Comment


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

          Comment

          Working...
          X