My greetings to the community,
I have the following questions regarding differential expressed genes (DEGs) with scvi:
From my understanding differential expression is an outcome of the generative process of scvi and as such fold-changes have a distribution. Although, we can look at the
lfc_medianto infer up or down regulation in the group of interest, my first question concerns the interpetation of the large ranges of fold-changes with
lfc_minbeing a negative and
lfc_maxa positive value. Would that be an indicator of uncertainty that could be fixed with larger sample size? In relation to this, the
bayes_factorin the vast majority of the DEGs is within the range 2-3. Would you put a threshold and consider DEGs only those with
bayes_factor >= 3to suggest substantial evidence of the alternative hypothesis?
I have observed DEGs where the
0.000000. Is this an indicator of an error, or is it due to six decimals approximation?
Thank you in advance,