I am sorry if this sounds like a stupid question, but I looked around and I could not find a proper answer.
Given idx1, idx2
as parameters to my my model.differential_expression
, if I find that for a given gene the LFC is positive, does it mean that it is over expressed in idx1
or idx2
?
In this tutorial it is stated that
Positive values of the LFC signify that the gene is upregulated in
idx1
.
However, looking in the documentation it is reported that the LFC is equal to log(B) - log(A)
with idx1
indicated as A and idx2
indicated as B. Following, I attach the corresponding pictures for clarity:
So, which one is correct? Looking at my data, it seems to that the second option (B over A, i.e. idx2 / idx1
it’s what is actually happening, buy I am not sure and I could not grasp it from the code.
Thank you in advance for any help.