problem of edgeR

[ptero...@gmail.com]

Hi Brian,

when I run abundance_estimates_to_matrix.pl, I get an error message as below:

-reading file: 1C_AB/abundance.tsv
-reading file: 1H_AB/abundance.tsv
-reading file: 5H_AB/abundance.tsv
-reading file: 6H_AB/abundance.tsv


* Outputting combined matrix.

/home/tools/trinityrnaseq-2.4.0/util/support_scripts/run_TMM_scale_matrix.pl --m
atrix kall.TPM.not_cross_norm > kall.TMM.EXPR.matrixCMD: R --vanilla -q < __tmp_
runTMM.R 1>&2
> library(edgeR)
Error in library(edgeR) : there is no package called 'edgeR'
Execution halted
Error, cmd: R --vanilla -q < __tmp_runTMM.R 1>&2  died with ret (256)  at /home/
tools/trinityrnaseq-2.4.0/util/support_scripts/run_TMM_scale_matrix.pl line 99.
Error, CMD: /home/tools/trinityrnaseq-2.4.0/util/support_scripts/run_TMM_scale_m
atrix.pl --matrix kall.TPM.not_cross_norm > kall.TMM.EXPR.matrix died with ret 6
400 at /home/tools/trinityrnaseq-2.4.0/util/abundance_estimates_to_matrix.pl lin
e 297.


I have installed R and packages, and made path for R (/usr/local/bin/R).
What else I can try?

Thanks very much!
Atsuko

[Brian Haas]

It looks like you need to install edgeR from bioconductor:

https://bioconductor.org/packages/release/bioc/html/edgeR.html

install by simply (from within R)

source("https://bioconductor.org/biocLite.R")
biocLite("edgeR")

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Brian J. Haas
The Broad Institute
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[Greg Andrews]

Hello,

I am having the same issue, although I have installed the required R packages as described in the documentation. For some reason this problem is just happening although I have used the Trinity DE pipeline before without a problem. Whenever I run a differential expression analysis script that requires a bioconductor package (edgeR, Biobase, etc), that package cannot be found. However, packages that come installed with R, such as 'cluster' can be found. Interestingly, when I'm in the command line version of R, and type 'library(Biobase), the library is found. Thanks so much for your help!

Greg

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[Atsuko Sato]

Hi Brian and Greg

Thanks for the suggestion - Just an update of my problem - I found that R and bioconductor packages were not installed in the node. Installing them into the node solved the problem!

Best wishes

Atsuko

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