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dviraran / SingleR

SingleR: Single-cell RNA-seq cell types Recognition (legacy version)
GNU General Public License v3.0
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Matrix dimension matching error #102

Closed ajwilk closed 5 years ago

ajwilk commented 5 years ago

Hi there, Been using SingleR on a number of datasets but running into a new error now: 

singler = SingleR(method = "single", combined.emat, ref_data$data, ref_data$main_types, clusters = NULL, genes = "de", quantile.use = 0.8, p.threshold = 0.05, fine.tune = FALSE, sd.thres = 1, do.pvals = T, numCores = 1)
[1] "Number of DE genes:3136"
[1] "Number of cells: 17829"
Error in cbind(r, cor(sc_data[, A], ref_data, method = "spearman")) : 
  number of rows of matrices must match (see arg 2)

I thought this may have been related to the size of the dataset, but the error is independent of numCores. Thoughts? Let me know what other info could be helpful, and happy to confidentially share data.

dviraran commented 5 years ago

Hi,

Since you are using the SingleR function, I would strongly recommend trying the new package that we are rolling out (soon on bioconductor) - https://github.com/LTLA/SingleR

Please let me know if there is still a problem.

Best, Dvir