Getting opposite log2 fold change
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leekun4 • 0
@leekun4-20057
Last seen 3.7 years ago

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.

deseq2 gene expression log2foldchange R • 1.8k views
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@mikelove
Last seen 1 minute ago
United States

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).

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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?

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Read the vignette section I mentioned in my answer twice.

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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.

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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.

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