I have RNA-seq data for samples in 10 different groups and I would like to find deferentially expressed genes. I have used Deseq2 R package. The deferentially expressed genes have FDR between 0.03 and 0.05. I checked log2FC and found it is low value in most deferentially expressed genes. How I can explain this? Why genes with low log2FC are found to be deferentially expressed? Also I have checked the normalized count and I couldn't find any reason!
•
written
by
star
1 answer
The number of groups you're using suggests that there's a lot of variance shrinkage going on, which is why you're picking up low fold-change differences. My guess is that you have relatively few replicates per group, which is causing aggressive fold-change shrinkage.
Log in to answer this question.
-
Benjamini–Hochberg correction, FDR in genes' expressions
written by gen92 •
-
Differentially gene expression analysis
written by Nai •
-
different number of DEGS between edger, deseq2, limma voom
written by eridanus •
-
Filter out DE genes with low counts in deseq2
written by tianshenbio
-
DEG from RPKM...
written by jabbari.parnian •
-
From DESeq2 normalized counts to heatmap in R
written by deniz •
-
Deseq2 positive results for genes highly variable between replicates
written by guillaume.rbt
-
Does FDR value change based Fold change cutoff?
written by Biologist
-
Filter by Fold change in DESeq2
written by EpiExplorer
-
Selecting between p.value, FDR, Bonferroni
written by niutster
How come no differentially expressed gene has fdr below 0.03? I guess you have some kind of filtering going on ..