Question: ERROR for Trinity abundance_estimates_to_matrix.pl
1
gravatar for felix.kuo.1211
2.9 years ago by
felix.kuo.121110 wrote:

This is the ERROR.

hadoop@Master:~/simple/DE$ /usr/local/soft/Trinity/util/abundance_estimates_to_matrix.pl --est_method RSEM --out_prefix Trinity_trans Ae.RSEM.isoforms.results AT.RSEM.isoforms.results Be.RSEM.isoforms.results BT.RSEM.isoforms.results Ce.RSEM.isoforms.results CT.RSEM.isoforms.results
-reading file: Ae.RSEM.isoforms.results
-reading file: AT.RSEM.isoforms.results
-reading file: Be.RSEM.isoforms.results
-reading file: BT.RSEM.isoforms.results
-reading file: Ce.RSEM.isoforms.results
-reading file: CT.RSEM.isoforms.results

* Outputting combined matrix.

/usr/local/soft/Trinity/util/support_scripts/run_TMM_scale_matrix.pl --matrix Trinity_trans.TPM.not_cross_norm > Trinity_trans.TMM.EXPR.matrixCMD: R --vanilla -q < __tmp_runTMM.R 1>&2
> library(edgeR)
Loading required package: limma
>
> rnaseqMatrix = read.table("Trinity_trans.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) : missing values not supported
Calls: DGEList -> .isAllZero
Execution halted
Error, cmd: R --vanilla -q < __tmp_runTMM.R 1>&2  died with ret (256)  at /usr/local/soft/Trinity/util/support_scripts/run_TMM_scale_matrix.pl line 99.
Error, CMD: /usr/local/soft/Trinity/util/support_scripts/run_TMM_scale_matrix.pl --matrix Trinity_trans.TPM.not_cross_norm > Trinity_trans.TMM.EXPR.matrix died with ret 6400 at /usr/local/soft/Trinity/util/abundance_estimates_to_matrix.pl line 297.

I have Google for "Error in .isAllZero(counts) : missing values not supported" But there isn't any information.

rna-seq • 1.8k views
ADD COMMENTlink modified 23 months ago by Biostar ♦♦ 20 • written 2.9 years ago by felix.kuo.121110

It's safe to say that the issue is not with your perl script, but with edgeR. Most likely, you have missing values or NA in your file "Trinity_trans.TPM.not_cross_norm". Check if you do, and if yes, remove them and it should work.

ADD REPLYlink written 2.9 years ago by berge201580

I just cant find "Trinity_trans.TPM.not_cross_norm". Is it in Trinity?

ADD REPLYlink written 2.9 years ago by felix.kuo.121110
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1023 users visited in the last hour