SCDE Package scde.error.models ERROR

Question

[shg018]

Hi everyone

I have been trying to use scde package for single cell differential analysis and I have been getting an error on using:

o.ifm <- scde.error.models(counts = cd, groups = sg, n.cores = 10, threshold.segmentation = TRUE, save.crossfit.plots = FALSE, save.model.plots = FALSE, verbose = 1)

The error is :

o.ifm <- scde.error.models(counts = cd, groups = sg, n.cores = 10, threshold.segmentation = TRUE, save.crossfit.plots = FALSE, save.model.plots = FALSE, verbose = 1) cross-fitting cells. Error in tapply(colnames(counts), groups, function(ids) { : arguments must have same length

which later makes it so that my counts have 51 columns but o.ifm model has just 40 rows. That is my later code doesn't work because of this. My question is basically, how do I rectify this?

Thanks!

Answer 1

[dfscruz]

Check that the column names in cd are in exactly the same order than in sg. I think I had some troubles with that in the past.