Entering edit mode
7.4 years ago
pbigbig
▴
250
Hi all,
I have some confusion regarding 2 ways of usage of analyze_diff_expr.pl
script in Trinity package.
- In the usage instruction resides within script, we have to input matrix file:
${name}.TMM.EXPR.matrix
, as in:
# Required: # # --matrix <string> TMM.EXPR.matrix # # Optional: # # -P <float> p-value cutoff for FDR (default: 0.001) # # -C <float> min abs(log2(a/b)) fold change (default: 2 (meaning 2^(2) or 4-fold). # # --output <float> prefix for output file (default: "diffExpr.P${Pvalue}_C${C}) #
- But as I learned from other guides, some used script
run_TMM_normalization_write_FPKM_matrix.pl
to perform TMM normalization, as in:
/run_TMM_normalization_write_FPKM_matrix.pl -‐matrix ${name}.counts.matrix -‐lengths trans_lengths.txt
And then use the output ${name}.counts.matrix.TMM_normalized.FPKM
as the input matrix for analyze_diff_expr.pl
.
I tried both matrices as input and they give quite similar heatmap pattern, despite that values varied between them. Could someone explain the different between ${name}.TMM.EXPR.matrix
and ${name}.counts.matrix.TMM_normalized.FPKM
?
Thank you very much!