ERROR for Trinity abundance_estimates_to_matrix.pl

Question

[felix.kuo.1211]

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.

[berge2015]

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.

[felix.kuo.1211]

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