How to perform comparison between two differentially expressed data

Question

[rishav513]

Hello all,

Greetings of the day.

I need help with differential expression analysis. Actually, I performed a differential expression analysis through limma comparing different conditions.

Now, I have 15 differentially expressed csv files and want to perform the comparison between these files.

For example:

I have one differentially expressed file named "Nong_ctrl_vs_Nong_3h.csv" (this file has a comparison between "Nong control condition" and "Nong 3h stress condition")
and another file named "IR50_ctrl_vs_IR50_3h.csv" (this file has a comparison between "IR50 control condition" and "IR50 3h stress condition").

Now, I want to compare these two files to find unique upregulated/downregulated genes among Nong 3h stress condition and IR50 3h stress condition.

How can I do this?

Any help would be appreciated.

Thanks

Answer 1

[i.sudbery]

Do you still have access to the original data files? The correct way to do this is by doing the DE analysis to directly ask about the difference you are interested in. This effectively comes down to the manipulating the design and contrasts to extract the desired combination of coefficients. It is described in the limma users manual, section 9.4.2, page 45.

[rishav513]

Yaa, I think the same way. Actually, I was thinking if it could be done with the help of these files also or not. Thank you