Koen Van den Berge

Hi Davide, In tradeSeq we're also using BiocParallel, e.g. https://github.com/statOmics/tradeSeq/blob/master/R/fitGAM.R#L227-L229. Sometimes, it seems like the parallelization gets stuck at a particular point and you could be waiting forever for the...

The high log-CPMs is indeed normal with 10x-like datasets because of shallow sequencing depth per cell. @lazappi Could you try plotting the zinbwave weights only for the zeros in the...

In the first set of plots, are those MA-plots? Or does `difference' mean something else than log FC in your plots? They are interesting...

@lazappi Thanks! Looks much better indeed. Are you willing to share the `DGEList` object that you used to create the BCV plot? The trend line issue is likely just a...

Hi @Jay-Leung, The Wald test indeed does not look at the directionality of the differences in average expression. You may be able to approximate this by using the log fold-changes...

This may be related to #50.