Question: Interpreting results of DESeq2, regarding baseMean and log2FoldChange.
0
gravatar for blastzone.heimerdinger
14 months ago by

Dear forum, 

Hello, I have a question regarding interpreting DESeq2 results regarding baseMean and log2FoldChange. I run DESeq() to perform differential expression analysis between group 1 and 2, and got the results like following, condition is c("1", "2"). 

  baseMean log2FoldChange lfcSE
A 1000 -0.80 0.15
B 400 0.60 0.14
C 500 0.80 0.20

I have a difficulty interpreting these, as it seems that baseMean represents mean of all participants (both group 1 and 2). I thought that "baseMean represents mean of group 1 (base level), and log2FoldChange indicate the change of group2 from group1." Is this interpretation correct? 

If correct, How should I interpret this baseMean? Is it just showing all the participants mean for reference? I don't think the result is showing that "log2FoldChange of group 2 from all the group baseMean". I hope I clarified my question well...

Thanks in advance.

deseq2 • 304 views
ADD COMMENTlink modified 14 months ago by Michael Love24k • written 14 months ago by blastzone.heimerdinger0
Answer: Interpreting results of DESeq2, regarding baseMean and log2FoldChange.
1
gravatar for Michael Love
14 months ago by
Michael Love24k
United States
Michael Love24k wrote:

See this link below which describes the variables:

https://bioconductor.org/packages/release/bioc/vignettes/DESeq2/inst/doc/DESeq2.html#access-to-all-calculated-values

It’s the mean of all samples in the dataset. We kept the same name as DESeq to avoid breaking MA plot code but there isn’t always a reference level in DESeq2 so we just use the mean of all normalized counts.

ADD COMMENTlink written 14 months ago by Michael Love24k

Thank you very much for the answer and pointing me to the right vignette! I read the section and still get confused about log2FoldChange ...  if I understand it correctly, ignoring the baseMean of all the samples displayed in the results() table, from the results we can conclude that "if baseMean of A in group 1 is 100, shrinked log2FoldChange is -0.80 +- 0.15, so group2 have baseMean of 174.1 (100*(1/2^0.80)), and SE of 100*(1/2^-0.65)=156.9 to 100*(1/2^-0.95)=193.2"? I hope this is correct ... Sorry if misunderstanding.

ADD REPLYlink modified 14 months ago • written 14 months ago by blastzone.heimerdinger0
1

Sure that looks right for translating the LFC point estimate and SE to the count scale.

ADD REPLYlink written 14 months ago by Michael Love24k
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