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problem in trinity differential gene expression protocol

After successful quantification of reads through trinity protocol., I tried to generate the count matrix through the provided perl script. as

perl /home/aasim/anaconda3/pkgs/trinity-2.5.1-0/opt/trinity-2.5.1/util/abundance_estimates_to_matrix.pl --est_method RSEM S1/S1.isoforms.results S2/S2.isoforms.results W1/W1isoforms.results W2/W2isoforms.results --gene_trans_map gene_trans_map --name_sample_by_basedir

It shows

reading file: S1/S1.isoforms.results

reading file: S2/S2.isoforms.results

-reading file: W1/W1isoforms.results

-reading file: W2/W2isoforms.results

  • Outputting combined matrix.

Then the following error is shown:

/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 installed edgeR through conda as . conda install -c montilab bioconductor-edger It showe me following information:

Solving environment: done

# All requested packages already installed.

which edgeR returns nothing. whereis edgeR returns "edgeR"

How to fix it?

How to fix it.

trinity dge
• 1,852 views • link
written by majeedaasim • majeedaasim

edgeRis an R package, not a command-line program. You have to load it within R:

library(edgeR)
• 1 views • link
written by h.mon h.mon

It is executed through the perl script provided by the Trinity developers. So running it through R is not a concern here.

• 1 views • link
written by majeedaasim • majeedaasim

Also when I tried to run edgeR through R, it says;

> library(edgeR)

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

• 1 views • link
written by majeedaasim • majeedaasim

When I triued to install it from bioconductor using 

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

It gives along list of errors like: 

/usr/bin/locale:88:20: error: stray '\10' in program
/usr/bin/locale:89:1: error: stray '\16' in program
/usr/bin/locale:89:4: error: stray '\16' in program
/usr/bin/locale:89:7: error: stray '\16' in program
/usr/bin/locale:89:10: error: stray '\16' in program
/usr/bin/locale:89:13: error: stray '\16' in program
/usr/bin/locale:89:14: error: stray '\30' in program
/usr/bin/locale:89:16: error: stray '\16' in program
/usr/bin/locale:89:17: error: stray '\20' in program
/usr/bin/locale:89:19: error: stray '\16' in program
/usr/bin/locale:89:20: error: stray '\10' in program
/usr/bin/locale:89:33: error: stray '\5' in program
/usr/bin/locale:89:36: error: stray '\270' in program
/usr/bin/locale:89:37: error: stray '\336' in program
/usr/bin/locale:89:38: error: stray '\377' in program
/usr/bin/locale:89:39: error: stray '\377' in program
/usr/bin/locale:89

then

In file included from /home/aasim/anaconda3/x86_64-conda_cos6-linux-gnu/include/c++/7.2.0/iomanip:43:0,
             from /home/aasim/R/x86_64-pc-linux-gnu-library/3.4/Rcpp/include/RcppCommon.h:61,
             from /home/aasim/R/x86_64-pc-linux-gnu-library/3.4/Rcpp/include/Rcpp.h:27,
             from utils.h:9,
             from R_add_prior_count.cpp:1:

again the list of error messages

In file included from /home/aasim/anaconda3/x86_64-conda_cos6-linux-gnu/include/c++/7.2.0/iomanip:43:0, from /home/aasim/R/x86_64-pc-linux-gnu-library/3.4/Rcpp/include/RcppCommon.h:61, from /home/aasim/R/x86_64-pc-linux-gnu-library/3.4/Rcpp/include/Rcpp.h:27, from utils.h:9, from R_add_prior_count.cpp:1:

this continues many times untill finally it returns:

    ERROR: compilation failed for package ‘edgeR’
* removing ‘/home/aasim/R/x86_64-pc-linux-gnu-library/3.4/edgeR’

System information is 

hereplatform       x86_64-pc-linux-gnu         
arch           x86_64                      
os             linux-gnu                   
system         x86_64, linux-gnu           
status                                     
major          3                           
minor          4.1                         
year           2017                        
month          06                          
day            30                          
svn rev        72865                       
language       R                           
version.string R version 3.4.1 (2017-06-30)
nickname       Single Candle
• 1 views • link
updated by Ram Ram • written by majeedaasim • majeedaasim

Hello majeedaasim!

Questions similar to yours can already be found at:

We have closed your question to allow us to keep similar content in the same thread.

If you disagree with this please tell us why in a reply below. We'll be happy to talk about it.

Cheers!

• 1 views • link
written by h.mon h.mon

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