high fold changes due to the low counts

Question

[tonja.r]

I computed log2 fold changes (which is normally distributed) of treated vs untreated. I standardized ((x-mean)/sd) it and computed the p-values based on the assumption of the normal distribution and z-scores. I got some quite high log2 fold changes mainly due to the low counts. Is there a possibility to account for the low-counts (e.g high counts) while computing fold changes or to model the log 2 fold change as another distribution ( like beta distribution) that will count for the low-counts?

(PS. I am aware of DESeq, GFOLD, edgeR. However, I need a simple (maybe not that robust and reliable) method to account for low counts while calculating the p-values)

Answer 1

[jianxing.tongji]

A reasonable model like DESeq, GFOLD or edgeR should not be cursed by low read counts. The calculation is not related to fold change.

Answer 2

[jianxing.tongji]

A reasonable model like DESeq, GFOLD or edgeR should not be cursed by low read counts. The calculation is not related to fold change.