problem in matrix generation after abundance estimation by RSEM?

Question

[majeedaasim]

I am performing a differential gene expression analysis for which I generated the count files through RSEM. Now to produce a count matrix from individual files I use the following perl script as provided in the Tinity website.

perl /home/aasim/anaconda3/pkgs/trinity-2.5.1-0/opt/trinity-2.5.1/util/abundance_estimates_to_matrix.pl --est_method RSEM --gene_trans_map Concatenate_master_assembly.fasta.gene_trans_map S1/RSEM.isoforms.results S2/RSEM.isoforms.results W1/RSEM.isoforms.results W2/RSEM.isoforms.results --name_sample_by_basedir

It give me the following following information

-reading file: S1/RSEM.isoforms.results

-reading file: S2/RSEM.isoforms.results

-reading file: W1/RSEM.isoforms.results

-reading file: W2/RSEM.isoforms.results

*Outputting combined matrix.

Then throws the error as:

/home/aasim/anaconda3/pkgs/trinity-2.5.1-0/opt/trinity-2.5.1/util/support_scripts/run_TMM_scale_matrix.pl --matrix RSEM.isoform.TPM.not_cross_norm > RSEM.isoform.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/aasim/anaconda3/pkgs/trinity-2.5.1-0/opt/trinity-2.5.1/util/support_scripts/run_TMM_scale_matrix.pl line 105.

Error, CMD: /home/aasim/anaconda3/pkgs/trinity-2.5.1-0/opt/trinity-2.5.1/util/support_scripts/run_TMM_scale_matrix.pl --matrix RSEM.isoform.TPM.not_cross_norm > RSEM.isoform.TMM.EXPR.matrix died with ret 6400 at /home/aasim/anaconda3/pkgs/trinity-2.5.1-0/opt/trinity-2.5.1/util/abundance_estimates_to_matrix.pl line 383.

I tried to install the edgeR package through conda as:

conda install -c bioconda bioconductor-edger

It showed that edgeR is already installed

Solving environment: done # All requested packages already installed.

In R, when I tried to load the library, it shows following

library(edgeR) Error in library(edgeR) : there is no package called ‘edgeR’

How to fix the issue

[h.mon]

The R you are trying to use is the same from the Trinity environment? What which R shows?

[majeedaasim]

which R returns the following /home/aasim/anaconda3/bin/R

[majeedaasim]

I see that there is edgeR package in anaconda3 named as "bioconductor-edger-3.14.0-0" Trinity is also present in anaconda3 It seem R is also operating from conda environment.

Then what is the problem

[h.mon]

Are you installing Trinity in a separate conda environment? Can you post all the commands from your pipeline? Including conda activate and similar.

Answer 1

[h.mon]

Install Trinity, R and edgeR all from conda. As you are using Trinity 2.5.1 (there are later versions already available at the repositories), install by:

conda create -n Trinity-2.5.1 trinity=2.5.1 bioconductor-edger
conda activate Trinity-2.5.1

This should install Trinity, R and edgeR. I didn't test to check if everything needed to run the differential expression pipeline is installed, but if not, install the remaining dependencies using conda.

I have deleted the two other related posts you made. Please provide feedback here if the solution works for you or not.