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Murali-group / Beeline

BEELINE: evaluation of algorithms for gene regulatory network inference
GNU General Public License v3.0
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Error with Monocle #25

Closed jlaw9 closed 5 years ago

jlaw9 commented 5 years ago

In runScribe.R, I'm getting this error at estimateDispersions: https://github.com/Murali-group/Beeline/blob/master/Algorithms/SCRIBE/runScribe.R#L119

Error in `[.data.frame`(`*tmp*`, res$mu == 0) : 
  undefined columns selected
Calls: estimateDispersions ... eval_tidy -> disp_calc_helper_NB -> [ -> [.data.frame

Looks like this is the line in their code where the problem is happening: https://github.com/cole-trapnell-lab/monocle-release/blob/7df105006756801a305ff43321b26d289cd6e890/R/expr_models.R#L470 According to this stack overflow question, I think they forgot a comma for indexing the dataframe.

I tried removing cells with all 0s and genes with all 0s, but that didn't help. Looks like there a couple of issues on Monocle with a similar problem, but there's no response from the developers.

This is the command I was running on csb2:

docker run --rm -v /data/jeff-law/projects/2019-04-single-cell/Beeline:/data/ monocle:base /bin/sh -c "time -v -o data/inputs/datasets/li-2017/SCRIBE/time0.txt Rscript runMonocle.R -e data/inputs/datasets/li-2017/SCRIBE/ExpressionData0.csv -c data/inputs/datasets/li-2017/SCRIBE/CellData0.csv -g data/inputs/datasets/li-2017/SCRIBE/GeneData.csv -o data/inputs/datasets/li-2017/SCRIBE/ -d 5 -l 0 -m ucRDI -x negbinomial.size --outFile outFile0.csv"
tmmurali commented 5 years ago

Which version of Monocle? Will using an earlier version help?

jlaw9 commented 5 years ago

Actually, I realized I hadn't removed the cells with all 0's. After I removed those, Monocle ran with no problems.

And we're using version 2.8.