GSEA not returning significant gene sets
0
0
Entering edit mode
4 weeks ago

I'm using GSEA for my RNA-Seq data to find significant pathways. The software instructs to use normalized count data so I used TMM normalization by edgeR. However, I don't get any significant gene sets based on FDR. What would be the problem if I use non-normalized counts with just low counts filtered out? Thank you.

GSEA • 400 views
ADD COMMENT
0
Entering edit mode

What exactly is your experiment and goal?

ADD REPLY
0
Entering edit mode

finding gene sets that are changed between the two experimental groups.

ADD REPLY
0
Entering edit mode

Not sure if the normalization method has an impact on GSEA results, but you can give it a try also by normalizing with DESeq2. Usually, that's what I do.

However, how many DEGs have you identified with your pipeline?

ADD REPLY
0
Entering edit mode

Using DESeq2, I found 138 upregulated genes and 118 downregulated genes. I'll try normalization with DESeq2 as well. Thanks.

ADD REPLY
0
Entering edit mode

how does the PCA of the normalized counts look? can you see the grouping of samples as per metadata/variables?

ADD REPLY
0
Entering edit mode

I haven't performed that yet, but I'll try. Thanks

ADD REPLY
0
Entering edit mode

QC like that should be done first, be sure to do that. Also, one would need details which GSEA implementation you did run and how you normalized data.

ADD REPLY

Login before adding your answer.

Traffic: 913 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6