Search
Question: How to filter glmTreat results by a false discovery rate (FDR) of 0.05
0
gravatar for mictadlo
6 weeks ago by
mictadlo0
mictadlo0 wrote:

Hello, Currenty, I call glmTreat method as following:

tr <- glmTreat(fit, contrast=B.LvsP, coef = 2, lfc=log2(1.5))
topTags(tr)

I discovered this paper and In the "Differential gene and microRNA expression" section they described that the differentially expressed genes (DEGs) were filtered using the glmTreat function in edgeR, which tests for significant differences relative to a set log2-fold change (logFC) cutoff of 0.5. Results were then filtered by a false discovery rate (FDR) of 0.05.

How did they performed the above task?

Thank you in advance.

ADD COMMENTlink modified 6 weeks ago by Aaron Lun17k • written 6 weeks ago by mictadlo0
1
gravatar for Aaron Lun
6 weeks ago by
Aaron Lun17k
Cambridge, United Kingdom
Aaron Lun17k wrote:

Seems pretty simple, just do lfc=0.5.

ADD COMMENTlink written 6 weeks ago by Aaron Lun17k
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: 153 users visited in the last hour