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Question: How to filter glmTreat results by a false discovery rate (FDR) of 0.05
0
12 months ago by

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?

modified 12 months ago by Aaron Lun21k • written 12 months ago by mictadlo0
1
12 months ago by
Aaron Lun21k
Cambridge, United Kingdom
Aaron Lun21k wrote:

Seems pretty simple, just do lfc=0.5.