Question: (Closed) Confusion regarding Trinity analyze_diff_expr.pl
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gravatar for pbigbig
3.9 years ago by
pbigbig210
United States
pbigbig210 wrote:

Hi all,

I have some confusion regarding 2 ways of usage of analyze_diff_expr.pl script in Trinity package.

  1. 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})
 #
  
  1. 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!

ADD COMMENTlink written 3.9 years ago by pbigbig210

Hello phuongbigbig!

Questions similar to yours can already be found at:

We have closed your question to allow us to keep similar content in the same thread.

If you disagree with this please tell us why in a reply below. We'll be happy to talk about it.

Cheers!

PS: Double post
ADD REPLYlink written 3.9 years ago by Dan D7.1k
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