scds creates sparse->dense coercion
0
0
Entering edit mode
@lluis-revilla-sancho
Last seen 3 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 • 83 views
ADD COMMENT

Login before adding your answer.

Traffic: 369 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6