Entering edit mode
Hi there, I am using muscat for differential expression analysis for single-cell data, and I got the error below. what's wrong here?
res<- pbDS(sce_pb, design = design, contrast = my.contrasts)
|==================================================================================================================================================| 100%
Error: BiocParallel errors
element index: 1, 2, 3, 4, 5, 6, ...
first error: subscript out of bounds
devtools::session_info()
─ Session info ──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
hash: eagle, pensive face, sweat droplets
setting value
version R version 4.1.2 (2021-11-01)
os Ubuntu 20.04.3 LTS
system x86_64, linux-gnu
ui RStudio
language (EN)
collate en_US.UTF-8
ctype en_US.UTF-8
tz Etc/UTC
date 2022-03-23
rstudio 2021.09.0+351 Ghost Orchid (server)
pandoc 2.14.0.3 @ /usr/lib/rstudio-server/bin/pandoc/ (via rmarkdown)
─ Packages ───────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
package * version date (UTC) lib source
abind 1.4-5 2016-07-21 [2] RSPM (R 4.1.0)
annotate 1.70.0 2021-05-19 [1] Bioconductor
AnnotationDbi 1.56.2 2021-11-09 [1] Bioconductor
assertthat 0.2.1 2019-03-21 [2] RSPM (R 4.1.0)
backports 1.3.0 2021-10-27 [2] RSPM (R 4.1.0)
beachmat 2.8.1 2021-08-12 [1] Bioconductor
beeswarm 0.4.0 2021-06-01 [1] RSPM (R 4.1.0)
Biobase * 2.54.0 2021-10-26 [1] Bioconductor
BiocGenerics * 0.40.0 2021-10-26 [1] Bioconductor
BiocNeighbors 1.10.0 2021-05-19 [1] Bioconductor
BiocParallel * 1.26.2 2021-08-22 [1] Bioconductor
BiocSingular 1.8.1 2021-06-08 [1] Bioconductor
Biostrings 2.62.0 2021-10-26 [1] Bioconductor
bit 4.0.4 2020-08-04 [2] RSPM (R 4.1.0)
bit64 4.0.5 2020-08-30 [2] RSPM (R 4.1.0)
bitops 1.0-7 2021-04-24 [2] RSPM (R 4.1.0)
blme 1.0-5 2021-01-05 [1] RSPM (R 4.1.0)
blob 1.2.2 2021-07-23 [2] RSPM (R 4.1.0)
boot 1.3-28 2021-05-03 [3] CRAN (R 4.1.2)
broom 0.7.10 2021-10-31 [2] RSPM (R 4.1.0)
cachem 1.0.6 2021-08-19 [2] RSPM (R 4.1.0)
callr 3.7.0 2021-04-20 [2] RSPM (R 4.1.0)
car 3.0-12 2021-11-06 [1] RSPM (R 4.1.0)
carData 3.0-5 2022-01-06 [1] RSPM (R 4.1.0)
caTools 1.18.2 2021-03-28 [2] RSPM (R 4.1.0)
cellranger 1.1.0 2016-07-27 [2] RSPM (R 4.1.0)
circlize 0.4.13 2021-06-09 [1] RSPM (R 4.1.0)
cli 3.1.0 2021-10-27 [2] RSPM (R 4.1.0)
clue 0.3-60 2021-10-11 [1] RSPM (R 4.1.0)
cluster 2.1.2 2021-04-17 [3] CRAN (R 4.1.2)
codetools 0.2-18 2020-11-04 [3] CRAN (R 4.1.2)
colorspace 2.0-2 2021-06-24 [2] RSPM (R 4.1.0)
colorway 0.2.0 2022-02-10 [1] Github (hypercompetent/colorway@8ba8f00)
ComplexHeatmap 2.10.0 2021-10-26 [1] Bioconductor
cowplot 1.1.1 2020-12-30 [2] RSPM (R 4.1.0)
crayon 1.4.2 2021-10-29 [2] RSPM (R 4.1.0)
data.table 1.14.2 2021-09-27 [2] RSPM (R 4.1.0)
DBI 1.1.1 2021-01-15 [2] RSPM (R 4.1.0)
dbplyr 2.1.1 2021-04-06 [2] RSPM (R 4.1.0)
DelayedArray 0.18.0 2021-05-19 [1] Bioconductor
DelayedMatrixStats 1.14.3 2021-08-26 [1] Bioconductor
deldir 1.0-6 2021-10-23 [2] RSPM (R 4.1.0)
desc 1.4.0 2021-09-28 [2] RSPM (R 4.1.0)
DESeq2 1.32.0 2021-05-19 [1] Bioconductor
devtools 2.4.2 2021-06-07 [2] RSPM (R 4.1.0)
digest 0.6.28 2021-09-23 [2] RSPM (R 4.1.0)
distributional 0.3.0 2022-01-05 [1] RSPM (R 4.1.0)
dittoSeq 1.7.0 2022-02-10 [1] Github (dtm2451/dittoSeq@b158b29)
doParallel 1.0.17 2022-02-07 [1] RSPM (R 4.1.0)
dplyr * 1.0.7 2021-06-18 [2] RSPM (R 4.1.0)
edgeR 3.34.1 2021-09-05 [1] Bioconductor
ellipsis 0.3.2 2021-04-29 [2] RSPM (R 4.1.0)
evaluate 0.14 2019-05-28 [2] RSPM (R 4.1.0)
fansi 0.5.0 2021-05-25 [2] RSPM (R 4.1.0)
farver 2.1.0 2021-02-28 [2] RSPM (R 4.1.0)
fastmap 1.1.0 2021-01-25 [2] RSPM (R 4.1.0)
fitdistrplus 1.1-6 2021-09-28 [2] RSPM (R 4.1.0)
forcats * 0.5.1 2021-01-27 [2] RSPM (R 4.1.0)
foreach 1.5.2 2022-02-02 [1] RSPM (R 4.1.0)
fs 1.5.0 2020-07-31 [2] RSPM (R 4.1.0)
future 1.23.0 2021-10-31 [2] RSPM (R 4.1.0)
future.apply 1.8.1 2021-08-10 [2] RSPM (R 4.1.0)
genefilter 1.74.1 2021-10-12 [1] Bioconductor
geneplotter 1.70.0 2021-05-19 [1] Bioconductor
generics 0.1.1 2021-10-25 [2] RSPM (R 4.1.0)
GenomeInfoDb * 1.30.1 2022-01-30 [1] Bioconductor
GenomeInfoDbData 1.2.7 2022-02-09 [1] Bioconductor
GenomicRanges * 1.44.0 2021-05-19 [1] Bioconductor
GetoptLong 1.0.5 2020-12-15 [1] RSPM (R 4.1.0)
ggbeeswarm 0.6.0 2017-08-07 [1] RSPM (R 4.1.0)
ggdist 3.1.0 2022-02-13 [1] RSPM (R 4.1.0)
ggplot2 * 3.3.5 2021-06-25 [2] RSPM (R 4.1.0)
ggprism 1.0.3.9000 2022-02-10 [1] Github (csdaw/ggprism@e21c3ee)
ggpubr 0.4.0 2020-06-27 [1] RSPM (R 4.1.0)
ggrepel 0.9.1 2021-01-15 [2] RSPM (R 4.1.0)
ggridges 0.5.3 2021-01-08 [2] RSPM (R 4.1.0)
ggsignif 0.6.3 2021-09-09 [1] RSPM (R 4.1.0)
glmmTMB 1.1.3 2022-03-13 [1] RSPM (R 4.1.0)
GlobalOptions 0.1.2 2020-06-10 [1] RSPM (R 4.1.0)
globals 0.14.0 2020-11-22 [2] RSPM (R 4.1.0)
glue 1.5.0 2021-11-07 [2] RSPM (R 4.1.0)
goftest 1.2-3 2021-10-07 [2] RSPM (R 4.1.0)
gplots 3.1.1 2020-11-28 [2] RSPM (R 4.1.0)
gridExtra 2.3 2017-09-09 [2] RSPM (R 4.1.0)
gtable 0.3.0 2019-03-25 [2] RSPM (R 4.1.0)
gtools 3.9.2 2021-06-06 [2] RSPM (R 4.1.0)
harmony * 0.1.0 2021-06-02 [1] RSPM (R 4.1.2)
haven 2.4.3 2021-08-04 [2] RSPM (R 4.1.0)
hdf5r 1.3.5 2021-11-15 [1] RSPM (R 4.1.0)
here * 1.0.1 2020-12-13 [2] RSPM (R 4.1.0)
hms 1.1.1 2021-09-26 [2] RSPM (R 4.1.0)
htmltools 0.5.2 2021-08-25 [2] RSPM (R 4.1.0)
htmlwidgets 1.5.4 2021-09-08 [2] RSPM (R 4.1.0)
httpuv 1.6.3 2021-09-09 [2] RSPM (R 4.1.0)
httr 1.4.2 2020-07-20 [2] RSPM (R 4.1.0)
ica 1.0-2 2018-05-24 [2] RSPM (R 4.1.0)
igraph 1.2.8 2021-11-07 [2] RSPM (R 4.1.0)
IRanges * 2.28.0 2021-10-26 [1] Bioconductor
irlba 2.3.3 2019-02-05 [2] RSPM (R 4.1.0)
iterators 1.0.14 2022-02-05 [1] RSPM (R 4.1.0)
janitor 2.1.0 2021-01-05 [1] RSPM (R 4.1.0)
jsonlite 1.7.2 2020-12-09 [2] RSPM (R 4.1.0)
KEGGREST 1.34.0 2021-10-26 [1] Bioconductor
KernSmooth 2.23-20 2021-05-03 [3] CRAN (R 4.1.2)
knitr 1.36 2021-09-29 [2] RSPM (R 4.1.0)
later 1.3.0 2021-08-18 [2] RSPM (R 4.1.0)
lattice 0.20-45 2021-09-22 [3] CRAN (R 4.1.2)
lazyeval 0.2.2 2019-03-15 [2] RSPM (R 4.1.0)
leiden 0.3.9 2021-07-27 [2] RSPM (R 4.1.0)
lifecycle 1.0.1 2021-09-24 [2] RSPM (R 4.1.0)
limma * 3.50.0 2021-10-26 [1] Bioconductor
listenv 0.8.0 2019-12-05 [2] RSPM (R 4.1.0)
lme4 1.1-28 2022-02-05 [1] RSPM (R 4.1.0)
lmerTest 3.1-3 2020-10-23 [1] RSPM (R 4.1.0)
lmtest 0.9-39 2021-11-07 [2] RSPM (R 4.1.0)
locfit 1.5-9.4 2020-03-25 [1] RSPM (R 4.1.0)
lubridate 1.8.0 2021-10-07 [2] RSPM (R 4.1.0)
magrittr 2.0.1 2020-11-17 [2] RSPM (R 4.1.0)
MASS 7.3-54 2021-05-03 [3] CRAN (R 4.1.2)
Matrix 1.3-4 2021-06-01 [3] CRAN (R 4.1.2)
MatrixGenerics * 1.4.3 2021-08-26 [1] Bioconductor
matrixStats * 0.61.0 2021-09-17 [2] RSPM (R 4.1.0)
memoise 2.0.0 2021-01-26 [2] RSPM (R 4.1.0)
mgcv 1.8-38 2021-10-06 [3] CRAN (R 4.1.2)
mime 0.12 2021-09-28 [2] RSPM (R 4.1.0)
miniUI 0.1.1.1 2018-05-18 [2] RSPM (R 4.1.0)
minqa 1.2.4 2014-10-09 [1] RSPM (R 4.1.0)
modelr 0.1.8 2020-05-19 [2] RSPM (R 4.1.0)
munsell 0.5.0 2018-06-12 [2] RSPM (R 4.1.0)
muscat * 1.8.2 2022-03-10 [1] Bioconductor
nlme 3.1-153 2021-09-07 [3] CRAN (R 4.1.2)
nloptr 2.0.0 2022-01-26 [1] RSPM (R 4.1.0)
numDeriv 2016.8-1.1 2019-06-06 [1] RSPM (R 4.1.0)
paletteer 1.4.0 2021-07-20 [1] RSPM (R 4.1.0)
parallelly 1.28.1 2021-09-09 [2] RSPM (R 4.1.0)
patchwork 1.1.1 2020-12-17 [2] RSPM (R 4.1.0)
pbapply 1.5-0 2021-09-16 [2] RSPM (R 4.1.0)
pbkrtest 0.5.1 2021-03-09 [1] RSPM (R 4.1.0)
pheatmap 1.0.12 2019-01-04 [1] RSPM (R 4.1.0)
pillar 1.6.4 2021-10-18 [2] RSPM (R 4.1.0)
pkgbuild 1.2.0 2020-12-15 [2] RSPM (R 4.1.0)
pkgconfig 2.0.3 2019-09-22 [2] RSPM (R 4.1.0)
pkgload 1.2.3 2021-10-13 [2] RSPM (R 4.1.0)
plotly 4.10.0 2021-10-09 [2] RSPM (R 4.1.0)
plyr 1.8.6 2020-03-03 [2] RSPM (R 4.1.0)
png 0.1-7 2013-12-03 [2] RSPM (R 4.1.0)
polyclip 1.10-0 2019-03-14 [2] RSPM (R 4.1.0)
presto 1.0.0 2022-02-23 [1] Github (immunogenomics/presto@052085d)
prettyunits 1.1.1 2020-01-24 [2] RSPM (R 4.1.0)
processx 3.5.2 2021-04-30 [2] RSPM (R 4.1.0)
progress 1.2.2 2019-05-16 [2] RSPM (R 4.1.0)
promises 1.2.0.1 2021-02-11 [2] RSPM (R 4.1.0)
ps 1.6.0 2021-02-28 [2] RSPM (R 4.1.0)
purrr * 0.3.4 2020-04-17 [2] RSPM (R 4.1.0)
R6 2.5.1 2021-08-19 [2] RSPM (R 4.1.0)
RANN 2.6.1 2019-01-08 [2] RSPM (R 4.1.0)
RColorBrewer 1.1-2 2014-12-07 [2] RSPM (R 4.1.0)
Rcpp * 1.0.7 2021-07-07 [2] RSPM (R 4.1.0)
RcppAnnoy 0.0.19 2021-07-30 [2] RSPM (R 4.1.0)
RCurl 1.98-1.6 2022-02-08 [1] RSPM (R 4.1.0)
readr * 2.1.0 2021-11-11 [2] RSPM (R 4.1.0)
readxl 1.3.1 2019-03-13 [2] RSPM (R 4.1.0)
rematch2 2.1.2 2020-05-01 [2] RSPM (R 4.1.0)
remotes 2.4.1 2021-09-29 [2] RSPM (R 4.1.0)
reprex 2.0.1 2021-08-05 [2] RSPM (R 4.1.0)
reshape2 1.4.4 2020-04-09 [2] RSPM (R 4.1.0)
reticulate 1.22 2021-09-17 [2] RSPM (R 4.1.0)
rjson 0.2.21 2022-01-09 [1] RSPM (R 4.1.0)
RSQLite 2.2.9 2021-12-06 [1] RSPM (R 4.1.0)
rstatix 0.7.0 2021-02-13 [1] RSPM (R 4.1.0)
rstudioapi 0.13 2020-11-12 [2] RSPM (R 4.1.0)
rsvd 1.0.5 2021-04-16 [1] RSPM (R 4.1.0)
Rtsne 0.15 2018-11-10 [2] RSPM (R 4.1.0)
rvest 1.0.2 2021-10-16 [2] RSPM (R 4.1.0)
S4Vectors * 0.32.3 2021-11-21 [1] Bioconductor
ScaledMatrix 1.0.0 2021-05-19 [1] Bioconductor
scales 1.1.1 2020-05-11 [2] RSPM (R 4.1.0)
scater 1.22.0 2021-10-26 [1] Bioconductor
scattermore 0.7 2020-11-24 [2] RSPM (R 4.1.0)
scCustomize * 0.7.0 2022-02-10 [1] Github (samuel-marsh/scCustomize@8414d1f)
sctransform 0.3.3 2022-01-13 [1] RSPM (R 4.1.0)
scuttle 1.2.1 2021-08-05 [1] Bioconductor
sessioninfo 1.2.1 2021-11-02 [2] RSPM (R 4.1.0)
Seurat * 4.1.0 2022-01-14 [1] RSPM (R 4.1.0)
SeuratDisk * 0.0.0.9019 2022-02-10 [1] Github (mojaveazure/seurat-disk@163f1aa)
SeuratObject * 4.0.4 2021-11-23 [1] RSPM (R 4.1.0)
shape 1.4.6 2021-05-19 [1] RSPM (R 4.1.0)
shiny 1.7.1 2021-10-02 [2] RSPM (R 4.1.0)
SingleCellExperiment * 1.14.1 2021-05-21 [1] Bioconductor
snakecase 0.11.0 2019-05-25 [1] RSPM (R 4.1.0)
sparseMatrixStats 1.4.2 2021-08-08 [1] Bioconductor
SummarizedExperiment * 1.22.0 2021-05-19 [1] Bioconductor
[1] /home/rstudio/R/x86_64-pc-linux-gnu-library/4.1-3.14
[2] /usr/local/lib/R/site-library
[3] /usr/local/lib/R/library
I also tried below before running pbDS. same error
library("BiocParallel")
registered()
serialParam <- SerialParam()
register(serialParam)
Thanks! Tommy
Thank you, Martin. Indeed, the design was wrong. it now works.