I am reading a paper that has a passage describing the pre-processing of gene expression data before conducting the experiments. The passage states "After conversion to a base-2 logarithm with a pseudo count of 0.125, batch normalization using ComBat was applied".

What exactly is a pseudo count? What I understood initially was that you add 0.125 to every value in your gene expression matrix and then take the logarithm of that to avoid taking the logarithm of 0 (which is not defined). This is based on my intuition though and I would like to know if this is correct and if there are other reasons why pseudo counts are used.


Your understanding is correct.

I personally like `log2(x+1)` because a pseudocount of 1 means you don't have to deal with negative numbers.