Question: errors in newCellDataSet Monocle function
1
gravatar for jonessara770
3 months ago by
jonessara770100
jonessara770100 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 • 180 views
ADD COMMENTlink modified 12 weeks ago by Batu40 • written 3 months ago by jonessara770100
0
gravatar for Batu
12 weeks ago by
Batu40
Batu40 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 12 weeks ago by Batu40
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1606 users visited in the last hour