Question: errors in newCellDataSet Monocle function
1
gravatar for jonessara770
4 weeks ago by
jonessara77070
jonessara77070 wrote:

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

rna-seq single cell • 90 views
ADD COMMENTlink modified 2 days ago by cakirb0 • written 4 weeks ago by jonessara77070
0
gravatar for cakirb
2 days ago by
cakirb0
Turkey/GTU
cakirb0 wrote:

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())
ADD COMMENTlink written 2 days ago by cakirb0
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