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PMBio / scLVM

scLVM is a modelling framework for single-cell RNA-seq data that can be used to dissect the observed heterogeneity into different sources, thereby allowing for the correction of confounding sources of variation.
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'module' object has no attribute 'CFixedCF' #17

Closed jkleinj closed 1 year ago

jkleinj commented 8 years ago

Dear Authors,

I am running the vignette https://github.com/PMBio/scLVM/blob/master/R/tutorials/scLVM_vignette.Rmd

on the current (cloned) version of scLVM https://github.com/PMBio/scLVM/blob/master/R/scLVM_0.99.2.tar.gz.

In the section 'Fitting multiple factors', the line % th2 = fitFactor(sclvmMult, idx = idx_Th2, XKnown = Xcc, k = 1, interaction=TRUE) returns an error message of the type % 'module' object has no attribute 'CFixedCF'.

Do you have an explanation and possibly a solution for that?

Thanks, Jens

arthuryxt commented 8 years ago

Dear Authors,

I am also stuck there. Could you fix it?

Thanks, Arthur

emerygoossens commented 8 years ago

I cannot seem to get past this part either. I am having trouble including additional covariates when using the fitFactor() function. In particular, when including a binary treatment/control vector, I get the following error.

CellCycle = fitFactor(sclvm,geneSet = ens_ids_cc,XKnown = cell_binary, k=1,use_ard = F)

Error in python.exec(paste("X,K,Kint,varGPLVM_ARD = ", objName, ".fitFactor(idx=idx, X0=X0, k=k,standardize=standardize, use_ard=use_ard, interaction=interaction, initMethod=initMethod)", : ufunc 'divide' output (typecode 'd') could not be coerced to provided output parameter (typecode 'l') according to the casting rule ''same_kind''

jshaik1979 commented 7 years ago

Same issue, has this been fixed? This is where it fails for me: th2 = fitFactor(sclvmMult, idx = idx_Th2, XKnown = Xcc, k = 1, interaction=TRUE)