Question: Concerning FDR calculation using Limma
gravatar for sebastien200109
5.4 years ago by
sebastien2001090 wrote:

I'm new to microarray and I'm trying to analyze several single channel agilent microarray using Limma package.
I have a question concerning the calculation of FDR q value using eBayes/topTable.
If I understood well, q value is an adjustment of p value linked to gene ranking. So, should the q value be calculated on an entire dataset or should it be calculated after filtering (removing non-coding RNA for instance)? As the number of variables will be different, the ranking should also be, will this impact the q value?


limma microarray fdr agilent • 1.9k views
ADD COMMENTlink modified 5.4 years ago • written 5.4 years ago by sebastien2001090

Just what I needed to know. Thank!

ADD REPLYlink written 5.4 years ago by sebastien2001090

If your problem got solved, please accept the answer by clicking on the green tick, which only you could see below the answer.

ADD REPLYlink modified 13 months ago by _r_am31k • written 5.4 years ago by Deepak Tanwar4.1k
gravatar for Devon Ryan
5.4 years ago by
Devon Ryan97k
Freiburg, Germany
Devon Ryan97k wrote:

You typically want to calculate q-values and adjusted p-values (they're different, though related) from your filtered dataset (assuming you're filtering by things like coding status or other factors independent from the p-value).

ADD COMMENTlink written 5.4 years ago by Devon Ryan97k
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