Search
Question: [Limma] Using P value or B statistics for cutoff?
0
gravatar for Wu, Xiwei
12.8 years ago by
Wu, Xiwei350
Wu, Xiwei350 wrote:

Hi,

I am using Limma to analyze my data, which is a simple two-group comparison (treated vs. control). The analysis is very straigtforward, but it becomes not as easy when the gene list is to be generated. I noticed that some genes with small P values (<0.05 adjusted with FDR) have negative B logodd scores, which mean the chance of DE is <50%. For situation like this, should I use log odd for cutoff or should I use P value or combined?

Xiwei Wu

ADD COMMENTlink modified 4 months ago by Gordon Smyth32k • written 12.8 years ago by Wu, Xiwei350
0
gravatar for Gordon Smyth
4 months ago by
Gordon Smyth32k
Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
Gordon Smyth32k wrote:

Dear Xiwei,

I wouldn't use the B statistic for cutoff because it depends on the prior probability that genes are DE, and this prior probability is by default just set to an arbitrary values (proportion=0.01).

So we usually use the FDR values to choose a cutoff.

In principle, you could use the propTrueHyp() function to estimate the prior probability that genes are DE, input this to eBayes() and then the B-statistic would be a meaningful cutoff. Usually though we prefer the FDR because it has a clear interpretation and doesn't require estimation of the prior probability.

ADD COMMENTlink modified 4 months ago • written 4 months ago by Gordon Smyth32k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.2.0
Traffic: 266 users visited in the last hour