David S. Fischer

Hi @jayypaul, this is hard to diagnose because it may be caused by very different issues. I would check the model: - Is the model (wald test formula) appropriate? You...

Hi @jayypaul, you might want to consult with a local statistician on this, as there are a lot of points to be cleared up. 1. Formula: You might want to...

Thanks for the PR @dburkhardt! I put this as `None` because t-test complains if it gets a noise model that is not gaussian. This way, t-test can always be run...

My take on the different tests is that they represent different assumptions on the data distribution and the necessity / way of inclusion of confounding variables. I agree with this...

Or just fit spline basis no set of unique continuous labels.

Hi @cchrysostomou, I recommend using Wald test for now, I am still working on gettting lrt to work in the new version, Wald is faster and preferable in my opinion...

I thought this was better dealt with here. I did not understand the question fully, what type of object would you want to call the volcano plot on? Right now...

Hi @jingxinfu! thanks for the comment! Two components here are - how to run multiple testing correction - this depends a bit whether one uses this functionality as a convenience...

I just want to add that fisher method https://docs.scipy.org/doc/scipy-0.16.0/reference/generated/scipy.stats.combine_pvalues.html is not very suitable here: if you want to have a single pvalue per gene, it s much cleaner to write...

Hi @wangjiawen2013, this depends on the noise model that you want to use. For most scenarios, I recommend negative binomial noise and for that you should provided unprocessed counts, ie...