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Wolfgang Huber
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@wolfgang-huber-3550
Last seen 3 months ago
EMBL European Molecular Biology Laborat…
I realize this is slightly out of scope since Seurat 2.3 is on CRAN, not Bioconductor, but given its developers recent interactions with the SIngleCellExperiment developers, I hope it's OK to post this here:
When trying to convert one of the Seurat data objects from the tabula muris, I get the following error. This seems to be related to the fact that the raw.data slot in this particular object is stored as a data.frame (rather than, say, matrix or dgCMatrix), which confuses the SummarizedExperiment constructor. A workaround is to convert the slot to a regular matrix before the conversion (see below). Perhaps it'd be a good idea to add that kind of workaround to the Seurat::as.SingleCellExperiment.seurat function (an alternative would be to clean the internet from legacy Seurat objects, which is perhaps less realistic?)
library("Seurat")
# from https://figshare.com/articles/Robject_files_for_tissues_processed_by_Seurat/5821263
load("facs_Liver_seurat_tiss.Robj")
tiss2 = tiss
tiss2@raw.data = as.matrix(tiss2@raw.data)
sc2 = as.SingleCellExperiment(tiss2)
sc = as.SingleCellExperiment(tiss)
#Error in seq_len(ncol(assay)) :
# argument must be coercible to non-negative integer
#In addition: Warning message:
#In seq_len(ncol(assay)) : first element used of 'length.out' argument
> devtools::session_info()
Session info ------------------------------------------------------------------
setting value
version R Under development (unstable) (2018-05-18 r74745)
system x86_64, darwin17.5.0
ui unknown
language (EN)
collate en_US.UTF-8
tz Europe/Berlin
date 2018-05-21
Packages ----------------------------------------------------------------------
package * version date source
abind 1.4-5 2016-07-21 CRAN (R 3.6.0)
acepack 1.4.1 2016-10-29 CRAN (R 3.6.0)
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assertthat 0.2.0 2017-04-11 CRAN (R 3.6.0)
backports 1.1.2 2017-12-13 CRAN (R 3.6.0)
base * 3.6.0 2018-05-19 local
base64enc 0.1-3 2015-07-28 CRAN (R 3.6.0)
bindr 0.1.1 2018-03-13 CRAN (R 3.6.0)
bindrcpp 0.2.2 2018-03-29 CRAN (R 3.6.0)
Biobase 2.41.0 2018-05-21 Bioconductor
BiocGenerics 0.27.0 2018-05-21 Bioconductor
BiocParallel 1.15.3 2018-05-21 Bioconductor
bitops 1.0-6 2013-08-17 CRAN (R 3.6.0)
broom 0.4.4 2018-03-29 CRAN (R 3.6.0)
caret 6.0-79 2018-03-29 CRAN (R 3.6.0)
caTools 1.17.1 2014-09-10 CRAN (R 3.6.0)
checkmate 1.8.5 2017-10-24 CRAN (R 3.6.0)
class 7.3-14 2015-08-30 CRAN (R 3.6.0)
cluster 2.0.7-1 2018-04-13 CRAN (R 3.6.0)
codetools 0.2-15 2016-10-05 CRAN (R 3.6.0)
colorspace 1.3-2 2016-12-14 CRAN (R 3.6.0)
compiler 3.6.0 2018-05-19 local
cowplot * 0.9.2 2017-12-17 CRAN (R 3.6.0)
CVST 0.2-1 2013-12-10 CRAN (R 3.6.0)
data.table 1.11.2 2018-05-08 CRAN (R 3.6.0)
datasets * 3.6.0 2018-05-19 local
ddalpha 1.3.3 2018-04-30 CRAN (R 3.6.0)
DelayedArray 0.7.0 2018-05-21 Bioconductor
DEoptimR 1.0-8 2016-11-19 CRAN (R 3.6.0)
devtools 1.13.5 2018-02-18 CRAN (R 3.6.0)
diffusionMap 1.1-0 2014-02-20 CRAN (R 3.6.0)
digest 0.6.15 2018-01-28 CRAN (R 3.6.0)
dimRed 0.1.0 2017-05-04 CRAN (R 3.6.0)
diptest 0.75-7 2016-12-05 CRAN (R 3.6.0)
doSNOW 1.0.16 2017-12-13 CRAN (R 3.6.0)
dplyr 0.7.5 2018-05-19 CRAN (R 3.6.0)
DRR 0.0.3 2018-01-06 CRAN (R 3.6.0)
dtw 1.20-1 2018-05-18 CRAN (R 3.6.0)
fitdistrplus 1.0-9 2017-03-24 CRAN (R 3.6.0)
flexmix 2.3-14 2017-04-28 CRAN (R 3.6.0)
FNN 1.1 2013-07-31 CRAN (R 3.6.0)
foreach 1.4.4 2017-12-12 CRAN (R 3.6.0)
foreign 0.8-70 2017-11-28 CRAN (R 3.6.0)
Formula 1.2-3 2018-05-03 CRAN (R 3.6.0)
fortunes * 1.5-4 2016-12-29 CRAN (R 3.6.0)
fpc 2.1-11 2018-01-13 CRAN (R 3.6.0)
gdata 2.18.0 2017-06-06 CRAN (R 3.6.0)
GenomeInfoDb 1.17.1 2018-05-21 Bioconductor
GenomeInfoDbData 1.1.0 2018-05-19 Bioconductor
GenomicRanges 1.33.5 2018-05-21 Bioconductor
geometry 0.3-6 2015-09-09 CRAN (R 3.6.0)
ggplot2 * 2.2.1 2016-12-30 CRAN (R 3.6.0)
ggridges 0.5.0 2018-04-05 CRAN (R 3.6.0)
glue 1.2.0 2017-10-29 CRAN (R 3.6.0)
gower 0.1.2 2017-02-23 CRAN (R 3.6.0)
gplots 3.0.1 2016-03-30 CRAN (R 3.6.0)
graphics * 3.6.0 2018-05-19 local
grDevices * 3.6.0 2018-05-19 local
grid 3.6.0 2018-05-19 local
gridExtra 2.3 2017-09-09 CRAN (R 3.6.0)
gtable 0.2.0 2016-02-26 CRAN (R 3.6.0)
gtools 3.5.0 2015-05-29 CRAN (R 3.6.0)
Hmisc 4.1-1 2018-01-03 CRAN (R 3.6.0)
htmlTable 1.11.2 2018-01-20 CRAN (R 3.6.0)
htmltools 0.3.6 2017-04-28 CRAN (R 3.6.0)
htmlwidgets 1.2 2018-04-19 CRAN (R 3.6.0)
ica 1.0-1 2015-08-25 CRAN (R 3.6.0)
igraph 1.2.1 2018-03-10 CRAN (R 3.6.0)
ipred 0.9-6 2017-03-01 CRAN (R 3.6.0)
IRanges 2.15.13 2018-05-21 Bioconductor
irlba 2.3.2 2018-01-11 CRAN (R 3.6.0)
iterators 1.0.9 2017-12-12 CRAN (R 3.6.0)
jsonlite 1.5 2017-06-01 CRAN (R 3.6.0)
kernlab 0.9-26 2018-04-30 CRAN (R 3.6.0)
KernSmooth 2.23-15 2015-06-29 CRAN (R 3.6.0)
knitr 1.20 2018-02-20 CRAN (R 3.6.0)
lars 1.2 2013-04-24 CRAN (R 3.6.0)
lattice 0.20-35 2017-03-25 CRAN (R 3.6.0)
latticeExtra 0.6-28 2016-02-09 CRAN (R 3.6.0)
lava 1.6.1 2018-03-28 CRAN (R 3.6.0)
lazyeval 0.2.1 2017-10-29 CRAN (R 3.6.0)
lmtest 0.9-36 2018-04-04 CRAN (R 3.6.0)
lubridate 1.7.4 2018-04-11 CRAN (R 3.6.0)
magic 1.5-8 2018-01-26 CRAN (R 3.6.0)
magrittr 1.5 2014-11-22 CRAN (R 3.6.0)
MASS 7.3-50 2018-04-30 CRAN (R 3.6.0)
Matrix * 1.2-14 2018-04-13 CRAN (R 3.6.0)
matrixStats 0.53.1 2018-02-11 CRAN (R 3.6.0)
mclust 5.4 2017-11-22 CRAN (R 3.6.0)
memoise 1.1.0 2017-04-21 CRAN (R 3.6.0)
metap 0.9 2018-04-25 CRAN (R 3.6.0)
methods * 3.6.0 2018-05-19 local
mixtools 1.1.0 2017-03-10 CRAN (R 3.6.0)
mnormt 1.5-5 2016-10-15 CRAN (R 3.6.0)
ModelMetrics 1.1.0 2016-08-26 CRAN (R 3.6.0)
modeltools 0.2-21 2013-09-02 CRAN (R 3.6.0)
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mvtnorm 1.0-7 2018-01-26 CRAN (R 3.6.0)
nlme 3.1-137 2018-04-07 CRAN (R 3.6.0)
nnet 7.3-12 2016-02-02 CRAN (R 3.6.0)
numDeriv 2016.8-1 2016-08-27 CRAN (R 3.6.0)
parallel 3.6.0 2018-05-19 local
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pillar 1.2.2 2018-04-26 CRAN (R 3.6.0)
pkgconfig 2.0.1 2017-03-21 CRAN (R 3.6.0)
plyr 1.8.4 2016-06-08 CRAN (R 3.6.0)
png 0.1-7 2013-12-03 CRAN (R 3.6.0)
prabclus 2.2-6 2015-01-14 CRAN (R 3.6.0)
prodlim 2018.04.18 2018-04-18 CRAN (R 3.6.0)
proxy 0.4-22 2018-04-08 CRAN (R 3.6.0)
psych 1.8.4 2018-05-06 CRAN (R 3.6.0)
purrr 0.2.4 2017-10-18 CRAN (R 3.6.0)
R.methodsS3 1.7.1 2016-02-16 CRAN (R 3.6.0)
R.oo 1.22.0 2018-04-22 CRAN (R 3.6.0)
R.utils 2.6.0 2017-11-05 CRAN (R 3.6.0)
R6 2.2.2 2017-06-17 CRAN (R 3.6.0)
ranger 0.9.0 2018-01-09 CRAN (R 3.6.0)
RANN 2.5.1 2017-05-21 CRAN (R 3.6.0)
RColorBrewer 1.1-2 2014-12-07 CRAN (R 3.6.0)
Rcpp 0.12.17 2018-05-18 CRAN (R 3.6.0)
RcppRoll 0.2.2 2015-04-05 CRAN (R 3.6.0)
RCurl 1.95-4.10 2018-01-04 CRAN (R 3.6.0)
recipes 0.1.2 2018-01-11 CRAN (R 3.6.0)
reshape2 1.4.3 2017-12-11 CRAN (R 3.6.0)
reticulate 1.7 2018-04-28 CRAN (R 3.6.0)
rlang 0.2.0 2018-02-20 CRAN (R 3.6.0)
robustbase 0.93-0 2018-04-24 CRAN (R 3.6.0)
ROCR 1.0-7 2015-03-26 CRAN (R 3.6.0)
rpart 4.1-13 2018-02-23 CRAN (R 3.6.0)
rstudioapi 0.7 2017-09-07 CRAN (R 3.6.0)
Rtsne 0.13 2017-04-14 CRAN (R 3.6.0)
S4Vectors 0.19.5 2018-05-21 Bioconductor
scales 0.5.0 2017-08-24 CRAN (R 3.6.0)
scatterplot3d 0.3-41 2018-03-14 CRAN (R 3.6.0)
SDMTools 1.1-221 2014-08-05 CRAN (R 3.6.0)
segmented 0.5-3.0 2017-11-30 CRAN (R 3.6.0)
Seurat * 2.3.1 2018-05-05 CRAN (R 3.6.0)
sfsmisc 1.1-2 2018-03-05 CRAN (R 3.6.0)
SingleCellExperiment 1.3.2 2018-05-21 Bioconductor
sn 1.5-2 2018-04-24 CRAN (R 3.6.0)
snow 0.4-2 2016-10-14 CRAN (R 3.6.0)
splines 3.6.0 2018-05-19 local
stats * 3.6.0 2018-05-19 local
stats4 3.6.0 2018-05-19 local
stringi 1.2.2 2018-05-02 CRAN (R 3.6.0)
stringr 1.3.1 2018-05-10 CRAN (R 3.6.0)
SummarizedExperiment 1.11.3 2018-05-21 Bioconductor
survival 2.42-3.1 2018-04-24 CRAN (R 3.6.0)
tclust 1.3-1 2017-08-24 CRAN (R 3.6.0)
tibble 1.4.2 2018-01-22 CRAN (R 3.6.0)
tidyr 0.8.1 2018-05-18 CRAN (R 3.6.0)
tidyselect 0.2.4 2018-02-26 CRAN (R 3.6.0)
timeDate 3043.102 2018-02-21 CRAN (R 3.6.0)
tools 3.6.0 2018-05-19 local
trimcluster 0.1-2 2012-10-29 CRAN (R 3.6.0)
tsne 0.1-3 2016-07-15 CRAN (R 3.6.0)
utils * 3.6.0 2018-05-19 local
VGAM 1.0-5 2018-02-07 CRAN (R 3.6.0)
withr 2.1.2 2018-03-15 CRAN (R 3.6.0)
XVector 0.21.1 2018-05-21 Bioconductor
zlibbioc 1.27.0 2018-05-21 Bioconductor
zoo 1.8-1 2018-01-08 CRAN (R 3.6.0)
See also https://github.com/satijalab/seurat/issues/485 and https://github.com/satijalab/seurat/pull/487