Question: How does limma calculate log-ratio of fold change?
0
gravatar for moradzadeh_k921
3.2 years ago by
moradzadeh_k9210 wrote:

Hello everybody

I faced a problem in analysis of the data set "GSE27274" by limma package. The parameter "Coef" which shows "logFC" calculated by limma  is different from the one I gained manually. I calculated log2 of treatment expression values average divided to control expression values average. I have not experienced this problem in analysis of other datasets. Is there any problem with my calculation?

Thank you

 

 

limma logfoldchange • 508 views
ADD COMMENTlink modified 3.2 years ago by Gordon Smyth38k • written 3.2 years ago by moradzadeh_k9210
Answer: How does limma calculate log-ratio of fold change?
1
gravatar for Gordon Smyth
3.2 years ago by
Gordon Smyth38k
Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
Gordon Smyth38k wrote:

Yes, there's a problem with your calculation. Assuming you are just comparing two groups, you need to log2 first, then average, not the other way around.

ADD COMMENTlink written 3.2 years ago by Gordon Smyth38k
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