errors in newCellDataSet Monocle function

Question

[jonessara770]

Hi I am newbie in using Monocle. Would you please help me with this error? The author said I should not use as.matrix for sparse matrix but the function will not work otherwise.

HSMM <- newCellDataSet(as(expr_matrix, "sparseMatrix"), phenoData = pd1, featureData = fd1, expressionFamily=negbinomial.size()) Error in as(from, "CsparseMatrix") : no method or default for coercing “data.frame” to “CsparseMatrix”

Thanks

Answer 1

[Batu]

Hello, seems like there is a missing part where you introduce a sparse matrix. Maybe it can be fixed when you change your code like this:

HSMM <- newCellDataSet(as(as.matrix(expr_matrix), "sparseMatrix"), phenoData = pd1, featureData = fd1, expressionFamily=negbinomial.size())