Jean Fan

Hi Poorya, Yes, lb, mle, ub represent the lower bound, maximum likelihood estimate, and upper bound of the 95% confidence interval for the expression fold change on log2 scale. Jean...

mle = maximum likelihood estimate of the fold change lb = lower bound estimate of the fold change ub = upper bound estimate of the fold change ce = conservative...

From Alexander: ``` I can add from my side, the same code worked with 4 cores (the maximal) on MacOS and it didn't on unix system (ncore set to 4...

- [x] GO enrichment testing does not work unless user has provided myGOTERM myGOTERM object not easily standardized since users provide the go environment Update: Addressed in `clean.go` where `annot...

- [ ] speed up the R code (a lot) by not calling R_CheckUserInterrupt(); in every single loop iteration but rather only every few thousand iterations. In particular, it’s most...

For those still experiencing errors with flexmix despite trying the solution from https://github.com/hms-dbmi/scde/issues/40 , can you please share your `sessionInfo()` ?

Hi Dave, Thanks for the thorough error report. I'm surprised the Docker container is also affected. Can you please try `knn.error.models` instead of `scde.error.models`? If a different error pops up,...

Hi Dave, Let me loop in Simon Steigler who made the Docker Container in case he has any advice or has seen this error before. Simon, do you happen to...

Hi Jean, Hi Dave, I am actually not sure whats going on here. I tried to reproduce your error, but with the docker I had to try out (R-3.4.1). I...

Hi Jens, If you look at the code for `pagoda.reduce.loading.redundancy`, you can see how the colors for the row cluster colors are determined. I've commented the relevant aspects of the...