Question: Getting opposite log2 fold change
0
gravatar for leekun4
6 weeks 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.

ADD COMMENTlink modified 6 weeks ago by Michael Love22k • written 6 weeks ago by leekun40
Answer: Getting opposite log2 fold change
0
gravatar for Michael Love
6 weeks ago by
Michael Love22k
United States
Michael Love22k 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).

ADD COMMENTlink modified 6 weeks ago • written 6 weeks ago by Michael Love22k

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?

ADD REPLYlink written 6 weeks ago by leekun40

Read the vignette section I mentioned in my answer twice.

ADD REPLYlink written 6 weeks ago by Michael Love22k

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?

Thank you for your time.

ADD REPLYlink written 6 weeks ago by leekun40

I'm not going to reply any more here. There are section of the vignette which directly answer your questions and I've pointed you to them.

ADD REPLYlink written 6 weeks ago by Michael Love22k
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