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shenorrLabTRDF / bseqsc

Bulk-Sequence Single-Cell Gene Expression Deconvolution Pipeline
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Error estimating proportions #5

Closed ONeillMB1 closed 6 years ago

ONeillMB1 commented 6 years ago

Thanks for developing this software!

I have successfully downloaded and run the pipeline from your tutorial on the sample data sets. When I try to perform the pipeline on my own data I get an error during the 'bseqsc_proportions' functions: 

> myfit <- bseqsc_proportions(bulkSet, scB, log=TRUE, verbose = TRUE)
* Data features: 'DPM1', 'SCYL3', ..., 'NEP' (11,561 total)
* Basis features: 'HA', 'RPL39', ..., 'RPL9' (38 total)
* Common features: 'GCLM', 'RPL6', ..., 'M2' (38 total)
* Converting to linear scale
* Writing input files ... OK
* Running CIBERSORT ... Error in if (max(Y) < 50) { : missing value where TRUE/FALSE needed

My 'bulkSet' has 11561 features, 957 samples and contains the corresponding expression matrix of log transformed TPM values. I am assuming there is something wrong with this ExpressionSet that I generated and/or the corresponding expression matrix, but the error message isn't too helpful in helping me identify what that might be. Any ideas? Thanks in advance.

ONeillMB1 commented 6 years ago

It is because I have zeros in my expression matrix. Closed.