Dan Sun comments

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                                            Dan Sun

error when run computeCommunProb function

Hello @sqjin! My data were batch-corrected by fastMNN, and therefore contained many negative values. Batch correction is quite important in my case as the two datasets I integrated had very...

[Chapter 6.3] Basic machine-learning approach freezing at end of first epoch

I ran into the same issue when using two GPUs. Not sure why, but after using only 1 GPU, it moved forward.

Update paramSweep.R

Will it be easier to use getAssayData(seu, assay = 'RNA', slot = 'counts') to avoid future code change due to different Seurat versions?

Error in reliability.test

Probably a sample size issue, and some of the folds may contain samples from only one level, thus failing the two-level requirement of roc().

Uninitalized value error post PE parsing

I am using exonerate 2.4, but still ran into the same problem. I think there is a memory issue associated with the usage of --bestn. I have more than 100Gb...