Hi everyone,

I have some confusion regarding two ways of usage of `analyze_diff_expr.pl`

script in the Trinity package.

In the usage instruction resides within script, we have to input matrix file: `${name}.TMM.EXPR.matrix`

, as following:

`# 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 values varied between them.
Could someone please explain the different between `${name}.TMM.EXPR.matrix`

and `${name}.counts.matrix.TMM_normalized.FPKM`

?

Thank you very much!

thank you for your suggestion !