Monocle3 error 'unable to find an inherited method for signature cell_data_set'

Question

[veravm13]

Hi, I'm trying to follow tutorial 1 on http://cole-trapnell-lab.github.io/monocle-release/monocle3/#tutorial-1-learning-trajectories-with-monocle-3, but when I try to use the functions estimateSizeFactors() on my CellDataSet, I get the error Error in (function (classes, fdef, mtable) : unable to find an inherited method for function ‘estimateSizeFactors’ for signature ‘"cell_data_set"’. I get the same error when trying to use the function estimateDispersions().

All I've done so far is (for as far as I am aware) successfully created a CellDataSet using the new_cell_data_set function..

I am using monocle3 0.2.2

My cds:

class: cell_data_set 
dim: 27998 6945 
metadata(1): cds_version
assays(1): counts
rownames(27998): ENSMUSG00000051951
  ENSMUSG00000089699 ... ENSMUSG00000096730
  ENSMUSG00000095742
rowData names(2): ENSID gene_short_name
colnames(6945): AAACCTGAGGCTATCT-1
  AAACCTGCACCAGGTC-1 ... TTTGTCATCATTTGGG-3
  TTTGTCATCCACTCCA-3
colData names(2): Cell Size_Factor
reducedDimNames(0):
spikeNames(0):
altExpNames(0):

Does anyone have any idea why it's not working?

Thanks!

[antonioggsousa]

Hi,

I just used once monocle so I'm not sure. Although DESeq2 has 2 functions with the same name. So, I don't know if monocle has 2 functions with the same name of DESeq2 or if it calls directly DESeq2.

Can you just confirm my theory by trying to see if you've DESeq2 installed, and if you don't have, can you install it and try it again.

From the error it seems that does not find the function, but I'm not quite sure either.

António

[veravm13]

Hi,

Thank you for your response. I think monocle uses these functions from the BiocGenerics package!

Best, Vera

[antonioggsousa]

Yes, DESeq2 is imported by BiocGenerics package. So I guess that it is still not working, right?

António

[veravm13]

I installed and loaded DESeq2 but I get the same error :(