scds creates sparse->dense coercion
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@lluis-revilla-sancho
Last seen 8 days ago
European Union

I am using R 4.4 and the latest version of scds (and Bioconductor). Whenever I run scds I get a warning:

sce2 <- bcds(gex, varImp = TRUE, retRes = TRUE)
## Warning messages:
## 1: In asMethod(object) :
##   sparse->dense coercion: allocating vector of size 11.7 GiB
sce2 <- cxds_bcds_hybrid(sce2, estNdbl = TRUE)
## Setting levels: control = 0, case = 1
## Setting direction: controls < cases
## Setting levels: control = 0, case = 1
## Setting direction: controls < cases
## Setting levels: control = 0, case = 1
## Setting direction: controls < cases
## Warning messages:
## 1: In stats::pbinom(as.matrix(obs) - 1, prob = prb, size = ncol(Bp),  :
##   partial argument match of 'log' to 'log.p'
## 2: In quantile.default(scrs_sim, prob = type) :
##   partial argument match of 'prob' to 'probs'
## 3: In quantile.default(scrs_sim, prob = type) :
##   partial argument match of 'prob' to 'probs'
## 4: In asMethod(object) :
##   sparse->dense coercion: allocating vector of size 11.7 GiB

Is there a way to avoid the conversion from sparse to dense?

scds • 596 views
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I think this is now preventing me to running in my dataset with 238578 cells, because I get an error: Error in Matrix::Matrix(counts(sce), sparse = TRUE) : data is too long

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