# Help with error during building an expression matrix

**URL:** <https://help.galaxyproject.org/t/help-with-error-during-building-an-expression-matrix/4341>\
**Category:** usegalaxy.org support\
**Tags:** transcriptomics, usinggalaxy, edger, limma\_voom\
**Created:** [August 24, 2020, 7:19am UTC](https://help.galaxyproject.org/t/help-with-error-during-building-an-expression-matrix/4341 "2020-08-24T07:19:31Z")\
**Posts on this page:** 2\
**Page:** 1

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**Author:** ![NITISH\_DAVE](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/nitish_dave/32/1334_2.png) [@NITISH\_DAVE](https://help.galaxyproject.org/u/NITISH_DAVE)\
**Post date:** [August 24, 2020, 7:19am UTC](https://help.galaxyproject.org/t/help-with-error-during-building-an-expression-matrix/4341/1 "2020-08-24T07:19:31Z")

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Hi, i am trying to build a expression matrix on galaxy platform but ending up with Fatal error: Exit code 25 () and couldn’t able to sort out the error. my input data is two abundance estimate output with tpm and fpkm values. it is showing a Common Potential Problem could be that the tool was executed with one or more duplicate input datasets. This frequently results in tool errors due to problematic input choices. (still i am not able to figure out what is wrong with the input file. please help.

-reading file: isoforms328  
-reading file: isoforms329

- Outputting combined matrix.

/cvmfs/main.galaxyproject.org/deps/\_conda/envs/mulled-v1-03aa6da237310bbe9f60ff3faf43ac3ceb173e3e63cc74bd3f93dd6d9587c3bd/opt/trinity-2.9.1/util/support\_scripts/run\_TMM\_scale\_matrix.pl --matrix RSEM.isoform.TPM.not\_cross\_norm \> RSEM.isoform.TMM.EXPR.matrixCMD: R --no-save --no-restore --no-site-file --no-init-file -q \< RSEM.isoform.TPM.not\_cross\_norm.runTMM.R 1\>&2

> library(edgeR)  
> Loading required package: limma
> 
> rnaseqMatrix = read.table(“RSEM.isoform.TPM.not\_cross\_norm”, header=T, row.names=1, com=‘’, check.names=F)  
> rnaseqMatrix = as.matrix(rnaseqMatrix)  
> rnaseqMatrix = round(rnaseqMatrix)  
> exp\_study = DGEList(counts=rnaseqMatrix, group=factor(colnames(rnaseqMatrix)))  
> Error in .isAllZero(counts) : counts must be positive finite values  
> Calls: DGEList → .isAllZero  
> Execution halted  
> Error, cmd: R --no-save --no-restore --no-site-file --no-init-file -q \< RSEM.isoform.TPM.not\_cross\_norm.runTMM.R 1\>&2 died with ret (256) at /cvmfs/main.galaxyproject.org/deps/\_conda/envs/mulled-v1-03aa6da237310bbe9f60ff3faf43ac3ceb173e3e63cc74bd3f93dd6d9587c3bd/opt/trinity-2.9.1/util/support\_scripts/run\_TMM\_scale\_matrix.pl line 105.  
> Error, CMD: /cvmfs/main.galaxyproject.org/deps/\_conda/envs/mulled-v1-03aa6da237310bbe9f60ff3faf43ac3ceb173e3e63cc74bd3f93dd6d9587c3bd/opt/trinity-2.9.1/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 /cvmfs/main.galaxyproject.org/deps/\_conda/envs/mulled-v1-03aa6da237310bbe9f60ff3faf43ac3ceb173e3e63cc74bd3f93dd6d9587c3bd/bin/abundance\_estimates\_to\_matrix.pl line 385.

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**Author:** ![BarreraLila](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/barreralila/32/2909_2.png) [@BarreraLila](https://help.galaxyproject.org/u/BarreraLila)\
**Post date:** [November 29, 2021, 1:55am UTC](https://help.galaxyproject.org/t/help-with-error-during-building-an-expression-matrix/4341/2 "2021-11-29T01:55:32Z")

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Hello,

I just ran into this issue and was wondering if you ever got this resolved or if you decided to go a different route with your analysis?

Thank you!  
LB