Question: Calculate the fold change between two groups
0
3.5 years ago by
ddzhangzz90
United States
ddzhangzz90 wrote:

Suppose I have gene expression values (not at log2) at pre and post from 3 patients (these are real values):

``````pre<-c(22.228, 0.002, 0.013)
post<-c(0.185, 0.018, 0.009)
``````

I am wondering how to calculate the mean fold change between pre and post:

``````#mean of fold change
mean(post/pre)
[1] 3.234
#fold change of mean
mean(post)/mean(pre)
[2] 0.0095
``````

Seems completely different, which one is the correct or should be calculated other ways?

If I wanted to calculate the log2FC:

``````#this seems the limma formula
mean(log2(post))-mean(log2(pre))
[1] -1.4231
#then back to fold change:
2^-1.4231
[1] 0.3729
``````

Why this 0.3729 is so different from either the other two 0.0095 and 3.234? Which way should I use?

rna-seq • 9.6k views
modified 3.5 years ago by Devon Ryan94k • written 3.5 years ago by ddzhangzz90
3
3.5 years ago by
Devon Ryan94k
Freiburg, Germany
Devon Ryan94k wrote:

`mean(post)/mean(pre)` is the fold-change. The log2 fold-change is `log2(mean(post)/mean(pre))`.

Thanks @Devon Ryan! Would you mind to provide some reference so I can check in details?

2

I wouldn't know what to reference for that, it's basic math. I should also note that you should not be calculating this yourself for RNAseq.