RNA-seq Differential analysis general question of interpreting data results.

Question

[lam.black.rider]

HI! Greetings to everybody.

I'm running a RNA-seq analysis and come to my mind a existential question, I have one group "control" and the experimental group "tricot" (my focus group). When I run:

$TRINITY_HOME/Analysis/DifferentialExpression/run_DE_analysis.pl

and then:

$TRINITY_HOME/Analysis/DifferentialExpression/analyze_diff_expr.pl

I got, for example the following gen:

which means that is sub-expressed, but what it means the digits under titles "treatment" "treatmen2"? So, this gen is sub-expressed in my treatment group?

because when I got the Heatmap the same gen is up-expressed following the color option:

where yellow is for treatment group (up-expressed) and purple (sub-express) for control which means the table is wrong or am I misunderstanding my results?

by the moment I appreciate your attention and any idea is well welcome :) .

-R

Answer 1

[swbarnes2]

At a glance, I'd say that expression for that gene is 0 in your controls, and higher in your Treatments. That would seem to agree with the heatmap image. The LogFC looks like it is comparing controls to treatment, which I'm guessing is not what you intended.

[lam.black.rider]

thank you very much I apreciate your answer, it helps me a lot to get a good idea about my data. greetings!