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tgen / bisbee

alternative splicing analysis pipeline
MIT License
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Error when running BisbeeDiff #6

Open Melebbi opened 2 years ago

Melebbi commented 2 years ago

Hi! I am new to BISBEE and I ran into some problems with bisbee diff. I followed the ReadMe file and generated the bisbeeCounts.csv file as descibed there.

As input for bisbeeDiff I used: Rscript stats/diff.R prep_A3.bisbeeCounts.csv sample_list.txt A3_DAS 200

where sample_list.txt is: ctrl_R1.markdup.sorted ctrl ctrl_R10.markdup.sorted ctrl ctrl_R2.markdup.sorted ctrl ctrl_R3.markdup.sorted ctrl ctrl_R4.markdup.sorted ctrl ctrl_R5.markdup.sorted ctrl mut_R10.markdup.sorted mut mut_R2.markdup.sorted mut mut_R3.markdup.sorted mut mut_R4.markdup.sorted mut mut_R5.markdup.sorted mut mut_R6.markdup.sorted mut

when I run it, I get the following Error multiple times: Error in solve.default(oout$hessian) : Lapack routine dgesv: system is exactly singular: U[1,1] = 0

the bisbee Diff file is nevertheless generated. What is the Error telling me in this context and can I still trust the generated BisbeeDiff file?

i don't know if this is the place for that kind of question, but I couldn't find anything helpful in the internet.

MattHuff commented 2 years ago

I am having the same issue with my data. However, it's not even producing a file for me; it's giving me an error about col.names:

Error in write.table(res, outname, col.names = cnames, row.names = FALSE,  : 
  invalid 'col.names' specification
Execution halted

While I suspect this may have something to do with the sample names, I've done my best to match my sample tables names to the examples in the GitHub page. There's little documentation elsewhere on the Internet, so this is the only place where I see someone having a similar error. If you have any guidance, please let me know.

ramikheireddine commented 12 months ago

how did you generate the sample.list.txt ?