Pierre-Luc

The current way these methods are implemented in `mmDS` do not support the use of contrasts, so you have to rely on the coefficients directly. Assuming that `group_idC` are your...

With `coef=c("group_idA")`, the p-value is that of a specific comparison (between A and the base factor level). Very leniently interpreted, it's the probability of having that difference between A and...

Hi, 1. Not at the moment. 2. This is indeed performed cluster-wise (for all methods). We reasoned that given the very important differences between cell types, there was no reason...

There seems to be nothing wrong with what you're doing, but I can't reproduce the bug neither in version 1.6.0 (Bioc) or 1.7.1 (Bioc-devel). Are you perhaps using an older...

On what OS are you running this? Depending on the platform BiocParallel sometimes has issues, especially when running it interactively from something like Rstudio, so you might try from the...

Hi, I'm encountering a similar error on a server that's behind an **http** proxy (the R proxy settings are configured accordingly). In our case, the problem is that in `list_ftp_dir`,...

Yes, it's a consequence of an http-only proxy (which is a pain, but not so uncommon either). I haven't tried, but I think a proxy that channels ftp as such...

It's not like I haven't tried complaining with the university IT already :) Personally I find a not-quite-robust solution that tends to work and sometimes fails is still better than...

Hi, First, just to be clear: you most likely have thousands of cells in that experiment, the overwhelming majority of which are in the lower-left corner, and another mode in...

Hi, Apologies for the delay. First I just want to note that your example is using an argument name (allsamples) that doesn't exist (I assume that's a mistake of putting...