fold-change or log2?-fold-change?

[TKuehnast]

In Differential Analysis/Associations you compare something like species between two conditions (healthy and sick). Namco can show p-values, fold-change and others.

Downloading the table, I saw values ranging from -1 to +1.
A fold-change from my understanding ranges from 0.0001 to 1 to 2 and above. No values become negative.

I assume its not fold change, but log-transformed fold-change? Importantly, its Log2-transformed?
Need the info for analysis and paper methods.

Thank you.

[alex-d13]

Hi,

For this part we use the SIAMCAT package. From what I now briefly read in their paper is that they use a generalized fold-change, which they reference to this publication.
Maybe you could check it for more details :)

The function description which we use (check.associations) also has some more detail on the topic:

the generalized fold change (gFC), a pseudo-fold change which is calculated as geometric mean of the differences between quantiles across both groups