understanding edgeR results

[Kishor Kumar Sarker]

Hi,
During a manual inspection of DE transcripts, I am having issues like:
1. I am getting the transcript beyond my threshold value (P1e-3)
2. Local running of edgeR is producing less number of transcripts
(from 1298 to 407) even at a less strict threshold (p<0.05).
For, example,

#In count matrix
TRINITY_DN66537_c0_g1_i1 47.917 52.304 29.235 14.958 13.681
[FW:0.000 0.000 0.000 0.000 0.000];[MW: 47.917 52.304 29.235
14.958 13.681]

#In TMM matrix
TRINITY_DN66537_c0_g1_i1
[FW:0.000 0.000 0.000 0.000 0.000];[MW:0.819 0.996 0.490
0.194 0.211]//Manual ttest value is 0.009//my threshold is P1e-3


#diffExpr.P1e-3_C2.matrix.log2.centered.dat
TRINITY_DN66537_c0_g1_i1
-0.296757129598697 -0.296757129598697 -0.296757129598697
-0.296757129598697 -0.296757129598697 0.566388413390702
0.700354591076477 0.27855520108874 -0.040954292995979
-0.0205582645664552


Can anyone please guide me on how to get the most accurate and
significant DE transcripts? Thank you.

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With best regards,

Kishor Kumar Sarker

PostDoc Fellow
Lab of Molecular Systematics and Ecology
Faculty of Life Sciences
Shanghai Ocean University, Shanghai, China
Phone: +8618621974360

[Brian Haas]

Hi Kishor,

Be sure to use the counts matrix as input to the DE analysis.  There should be an R script that's created in and executed for running the DE step. You can examine that R script to see how it might differ from how you're running it separately.

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Brian J. Haas
The Broad Institute
http://broadinstitute.org/~bhaas