Question: Differential expression analysis on Trinity tool
gravatar for iamtuttu5
3.0 years ago by
United States
iamtuttu540 wrote:

Hello all

I am using trinity tool for analyzing RNAseq data from ion proton

currently i am running command ,

command used :

 ~/trinityrnaseq-2.0.6/Analysis/DifferentialExpression/ --matrix /home/tuttu/Trinity_cardop12.counts.matrix.TMM_normalized.FPKM -C 2 -P 0.001 --output cluster_result

but it results an errorr

This is the errorr obtained

Error, no differentially expressed transcripts identified at cuttoffs: P:0.001, C:2 at /home/tuttu/trinityrnaseq-2.0.6/Analysis/DifferentialExpression/ line 198.


Anyone please help me on this

Thanks in advance






ADD COMMENTlink modified 3.0 years ago by Biogeek330 • written 3.0 years ago by iamtuttu540

This looks like a problem with your environment and working directory, not with the .pl script itself. Are you 100% sure you have established your working directory and paths correctly? I think it's a matter of showing the .pl where your file actually is.

ADD REPLYlink written 3.0 years ago by Biogeek330
gravatar for Biogeek
3.0 years ago by
Biogeek330 wrote:




cd $myjobdir


Try additionally putting these into your job file. I think the .pl is looking in the wrong palce as you haven't gave it a home directory or path.


ADD COMMENTlink written 3.0 years ago by Biogeek330

dear biogeek89

Thank you so much for the prompt reply

Now the command gives the following errorr


command used :

~/trinityrnaseq-2.0.6/Analysis/DifferentialExpression/ --matrix /home/tuttu/card.counts.matrix.TMM_normalized.FPKM -C 2 -P 0.001

Result obtained :


** Found 331 features as differentially expressed.

CMD: /home/tuttu/trinityrnaseq-2.0.6/Analysis/DifferentialExpression/PtR -m diffExpr.P0.001_C2.matrix --log2 --heatmap --min_colSums 0 --min_rowSums 0 --gene_dist euclidean --sample_dist euclidean --sample_cor_matrix --center_rows --save
CMD: R --vanilla -q < diffExpr.P0.001_C2.matrix.R
> library(cluster)
> library(Biobase)
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: ‘BiocGenerics’

The following objects are masked from ‘package:parallel’:

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following object is masked from ‘package:stats’:


The following objects are masked from ‘package:base’:

    anyDuplicated, append,, as.vector, cbind, colnames,
    duplicated, eval, evalq, Filter, Find, get, intersect, is.unsorted,
    lapply, Map, mapply, match, mget, order, paste, pmax,,
    pmin,, Position, rank, rbind, Reduce,, rownames,
    sapply, setdiff, sort, table, tapply, union, unique, unlist

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

> library(qvalue)
Error in library(qvalue) : there is no package called ‘qvalue’
Execution halted
Error, cmd: R --vanilla -q < diffExpr.P0.001_C2.matrix.R died with ret 256 at /home/tuttu/trinityrnaseq-2.0.6/Analysis/DifferentialExpression/PtR line 1568.
Error, Error, cmd: /home/tuttu/trinityrnaseq-2.0.6/Analysis/DifferentialExpression/PtR -m diffExpr.P0.001_C2.matrix --log2 --heatmap --min_colSums 0 --min_rowSums 0 --gene_dist euclidean --sample_dist euclidean --sample_cor_matrix --center_rows --save  died with ret 6400 at /home/tuttu/trinityrnaseq-2.0.6/Analysis/DifferentialExpression/ line 267.






ADD REPLYlink written 2.9 years ago by iamtuttu540
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