error abundance_estimates_to_matrix.pl count matrix error

[Nikelle Petrillo]

Hello, 

I am trying to generate a count matrix using abundance_estimates_to_matrix.pl script in Trinity, but I keep running into the same error. I fed the script two RSEM.genes.results files: 

$ perl /usr/local/bin/trinityrnaseq-2.0.6/util/abundance_estimates_to_matrix.pl --est_method RSEM --name_sample_by_basedir  ~/aligning/aligning5/RSEM.genes.results ~/aligning/aligning6/RSEM.genes.results 

-reading file: /home/npetrill/aligning/aligning5/RSEM.genes.results

-reading file: /home/npetrill/aligning/aligning6/RSEM.genes.results

* Outputting combined matrix.

/usr/local/bin/trinityrnaseq-2.0.6/util/support_scripts/run_TMM_scale_matrix.pl --matrix matrix.not_cross_norm.fpkm.tmp > matrix.TMM.fpkm.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 /usr/local/bin/trinityrnaseq-2.0.6/util/support_scripts/run_TMM_scale_matrix.pl line 98.

Error, CMD: /usr/local/bin/trinityrnaseq-2.0.6/util/support_scripts/run_TMM_scale_matrix.pl --matrix matrix.not_cross_norm.fpkm.tmp > matrix.TMM.fpkm.matrix died with ret 6400 at /usr/local/bin/trinityrnaseq-2.0.6/util/abundance_estimates_to_matrix.pl line 240.

Can anybody make sense of this for me? Also, A matrix.counts file was generated, however, there are NA's in the table. Does anyone know why this is?

Thanks for your help, Nikelle

[Mark Chapman]

Hi Kel,

NAs can happen if there's very little expression shared amongst your .results files. This can happen if you've generated separate trinity assemblies for each sample of if your two files are from expression of two very different individuals. Are either of these likely the cause?

Cheers, Mark

On 7 September 2016 at 04:34, Kelli Anderson <ando....@gmail.com> wrote:

Hi Nikelle,

Just wondering if you got to the bottom of this? I've just come across the same error.

Kel

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