Differential expression analysis on Trinity tool

Question

[iamtuttu5]

Hello all

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

Currently I am running analyze_diff_expr.pl command,

Command used:

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

But it results an error

This is the error obtained:

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

Anyone please help me on this

Thanks in advance

[Biogeek]

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.

Answer 1

[Biogeek]

myjobdir=/home/tuttu/

cd $myjobdir
PATH=://trinityrnaseq-2.0.6/Analysis/DifferentialExpression/:/home/tuttu:$PATH

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

[iamtuttu5]

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/analyze_diff_expr.pl --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':

    xtabs

The following objects are masked from 'package:base':

    anyDuplicated, append, as.data.frame, as.vector, cbind, colnames,
    duplicated, eval, evalq, Filter, Find, get, intersect, is.unsorted,
    lapply, Map, mapply, match, mget, order, paste, pmax, pmax.int,
    pmin, pmin.int, Position, rank, rbind, Reduce, rep.int, 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/analyze_diff_expr.pl line 267.