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Old 06-29-2015, 09:07 AM   #121
dpryan
Devon Ryan
 
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How did you make "rld" and what version of DESeq2 are you using?
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Old 06-29-2015, 09:14 AM   #122
Caitriona McEvoy
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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
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Old 07-01-2015, 07:44 AM   #123
Michael Love
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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It looks like you have a mix of out-of-date and new packages.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()
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Old 07-06-2015, 01:45 AM   #124
Caitriona McEvoy
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Hi Michael, Thank you for your reply. I installed packages as suggested, and it's working. Thanks! Caitriona
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