Question: Up and down regulated genes in deseq2
0
gravatar for anaQ
5 weeks ago by
anaQ0
anaQ0 wrote:

This is the command line I used in order to obtain the up and down regulated genes, after extracting the differentially expressed genes:

up <- subset(resultsDEG, log2FoldChange > 0)

down <- subset(resultsDEG, log2FoldChange < 0)

I'd like to know if i'm doing this right because somewhere i don't remember i saw that setting the cuttof to 0 it's fine. But now i'm not sure if i should use a different cutoff instead of 0. I have 3 replicates per sample.

ADD COMMENTlink modified 5 weeks ago by Michael Love23k • written 5 weeks ago by anaQ0
Answer: Up and down regulated genes in deseq2
0
gravatar for Michael Love
5 weeks ago by
Michael Love23k
United States
Michael Love23k wrote:

Take a look at the DESeq2 workflow, we go over interpreting the results including the LFC. Yes positive LFC is up regulation relative to the reference group.

ADD COMMENTlink written 5 weeks ago by Michael Love23k
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