Question: errors in newCellDataSet Monocle function
1
gravatar for jonessara770
8 months ago by
jonessara770130
jonessara770130 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 • 364 views
ADD COMMENTlink modified 7 months ago by Batu110 • written 8 months ago by jonessara770130
0
gravatar for Batu
7 months ago by
Batu110
Batu110 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 7 months ago by Batu110
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