Question: Getting opposite log2 fold change
0
3 months ago by
leekun40
leekun40 wrote:

I am currently doing DESeq2 analysis, and I am getting opposite log2 fold change when I plot on Volcano plot.

For example, one of my genes is down-regulated (with significant p-value) according to DESeq2; however, it says otherwise when I look at the actual gene expression data.

What am I doing wrong? Thanks for your help.

modified 3 months ago by Michael Love23k • written 3 months ago by leekun40
Answer: Getting opposite log2 fold change
0
3 months ago by
Michael Love23k
United States
Michael Love23k wrote:

Take a look at the vignette note on factor levels, and also see what is printed at the top of your results table when you print it in the console:

> res


This is an indicator for the user to know what R used as the reference level if you did not set it yourself (again see vignette note).

I really appreciate your help. When I typed res, I got this message:

log2 fold change (MLE): dex uninfected vs infected Wald test p-value: dex uninfected vs infected DataFrame with 6 rows and 6 columns

Any suggestions?

Hi Michael,

I wasn't sure what you meant by that (I'm new to coding). I found out that it's doing uninfected vs infected instead of infected vs uninfected.

res <-results(dds, contrast = list("infected", "uninfected"))


I tried this to change but i'm getting an error. Any suggestions?