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!