Error in running DESeq2 R script from Trinity pipeline: rowSums cpm

[aileen]

Hi Brian,

I’m hoping to use the R script from the Trinity pipeline in performing DESeq2 in Rstudio (modified to include batch in the design formula). Before doing so, I tried to replicate the said R script but I encountered the following error in this particular line:

rnaseqMatrix = rnaseqMatrix[rowSums(cpm(rnaseqMatrix) > 1) >= 2,] 

Error in h(simpleError(msg, call)) : 

  error in evaluating the argument 'x' in selecting a method for function 'rowSums': could not find function "cpm"

If I understand correctly, this is a filtering step to remove low counts (i.e. only keep genes with at least 1 CPM, in at least 2 samples)? I was not able to get the same results when I skipped this line. May I ask where I can find the function "cpm"?

Thank you in advance!

Best regards,
Aileen

[Ken Field]

The cpm function is part of the edgeR package. You must have had an error loading that package.

-Ken

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[aileen]

Hi Ken,

Thank you for the reply! I'm sorry for the basic question; this means I still run edgeR/this function even if I am performing DESeq2?  

Thank you very much!

Best, 

Aileen 

[Ken Field]

Yes. There is no equivalent function in the DESeq2 package so Trinity uses the edgeR function. It is still using DESeq2 for the differential expression analysis.

Ken

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[aileen]

Understood, thank you so much!

Best,

Aileen

[Brian Haas]

Thanks, Ken!!

~b

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Brian J. Haas
The Broad Institute
http://broadinstitute.org/~bhaas

 

[aileen]

Hi Brian/Ken,

In the R script from the same step run_DE_analysis.pl, may I ask where I can find the R script for the MA and Volcano plots?

"/usr/local/bin/trinityrnaseq/Analysis/DifferentialExpression/R/rnaseq_plot_funcs.R"

Thank you!

Best regards,

Aileen