Closed wfma closed 4 years ago
rj-patrick
commented
4 years ago Hi Wei,
I suspect this is due to the version of your STRINGdb package - I've made a change so that whatever version is available to you should be used by default. Please reinstall and let me know if the change fixes your issue.
Cheers,
Ralph
wfma
commented
4 years ago Hello!
I just reinstalled scTalk and updated STRINGdb via bioconductor. I am still getting the same error. I have attached my session info below;
─ Session info ──────────────────────────────────────────────────────────────────────────────────────────────────
setting value
version R version 4.0.0 (2020-04-24)
os macOS Catalina 10.15.5
system x86_64, darwin17.0
ui RStudio
language (EN)
collate en_US.UTF-8
ctype en_US.UTF-8
tz America/New_York
date 2020-06-30
─ Packages ──────────────────────────────────────────────────────────────────────────────────────────────────────
! package * version date lib source
abind 1.4-5 2016-07-21 [1] CRAN (R 4.0.0)
AnnotationDbi 1.50.0 2020-04-27 [1] Bioconductor
AnnotationHub 2.20.0 2020-04-27 [1] Bioconductor
ape 5.4 2020-06-03 [1] CRAN (R 4.0.0)
assertthat 0.2.1 2019-03-21 [1] CRAN (R 4.0.0)
backports 1.1.8 2020-06-17 [1] CRAN (R 4.0.0)
Biobase * 2.48.0 2020-04-27 [1] Bioconductor
BiocFileCache 1.12.0 2020-04-27 [1] Bioconductor
BiocGenerics * 0.34.0 2020-04-27 [1] Bioconductor
BiocManager 1.30.10 2019-11-16 [1] CRAN (R 4.0.0)
BiocNeighbors 1.6.0 2020-04-27 [1] Bioconductor
BiocParallel 1.22.0 2020-04-27 [1] Bioconductor
BiocSingular 1.4.0 2020-04-27 [1] Bioconductor
BiocVersion 3.11.1 2020-04-07 [1] Bioconductor
bit 1.1-15.2 2020-02-10 [1] CRAN (R 4.0.0)
bit64 0.9-7 2017-05-08 [1] CRAN (R 4.0.0)
bitops 1.0-6 2013-08-17 [1] CRAN (R 4.0.0)
blob 1.2.1 2020-01-20 [1] CRAN (R 4.0.0)
broom 0.5.6 2020-04-20 [1] CRAN (R 4.0.0)
callr 3.4.3 2020-03-28 [1] CRAN (R 4.0.0)
car 3.0-8 2020-05-21 [1] CRAN (R 4.0.0)
carData 3.0-4 2020-05-22 [1] CRAN (R 4.0.0)
caTools 1.18.0 2020-01-17 [1] CRAN (R 4.0.0)
cellranger 1.1.0 2016-07-27 [1] CRAN (R 4.0.0)
celltalker * 0.0.3.9000 2020-06-29 [1] Github (arc85/celltalker@533b28e)
chron 2.3-55 2020-02-02 [1] CRAN (R 4.0.0)
circlize * 0.4.10 2020-06-15 [1] CRAN (R 4.0.0)
class 7.3-17 2020-04-26 [1] CRAN (R 4.0.0)
cli 2.0.2 2020-02-28 [1] CRAN (R 4.0.0)
cluster 2.1.0 2019-06-19 [1] CRAN (R 4.0.0)
codetools 0.2-16 2018-12-24 [1] CRAN (R 4.0.0)
colorspace 1.4-1 2019-03-18 [1] CRAN (R 4.0.0)
cowplot 1.0.0 2019-07-11 [1] CRAN (R 4.0.0)
crayon 1.3.4 2017-09-16 [1] CRAN (R 4.0.0)
crosstalk 1.1.0.1 2020-03-13 [1] CRAN (R 4.0.0)
curl 4.3 2019-12-02 [1] CRAN (R 4.0.0)
data.table * 1.12.8 2019-12-09 [1] CRAN (R 4.0.0)
DBI 1.1.0 2019-12-15 [1] CRAN (R 4.0.0)
dbplyr 1.4.4 2020-05-27 [1] CRAN (R 4.0.0)
DelayedArray * 0.14.0 2020-04-27 [1] Bioconductor
DelayedMatrixStats 1.10.0 2020-04-27 [1] Bioconductor
DEoptimR 1.0-8 2016-11-19 [1] CRAN (R 4.0.0)
desc 1.2.0 2018-05-01 [1] CRAN (R 4.0.0)
devtools * 2.3.0 2020-04-10 [1] CRAN (R 4.0.0)
digest 0.6.25 2020-02-23 [1] CRAN (R 4.0.0)
diptest 0.75-7 2016-12-05 [1] CRAN (R 4.0.0)
dplyr * 1.0.0 2020-05-29 [1] CRAN (R 4.0.0)
dtplyr * 1.0.1 2020-01-23 [1] CRAN (R 4.0.0)
dynguidelines 1.0.0 2020-06-08 [1] Github (dynverse/dynguidelines@5181f75)
dynutils 1.0.5.9000 2020-06-08 [1] Github (dynverse/dynutils@dd41768)
ellipsis 0.3.1 2020-05-15 [1] CRAN (R 4.0.0)
ExperimentHub 1.14.0 2020-04-27 [1] Bioconductor
factoextra 1.0.7 2020-04-01 [1] CRAN (R 4.0.0)
fansi 0.4.1 2020-01-08 [1] CRAN (R 4.0.0)
farver 2.0.3 2020-01-16 [1] CRAN (R 4.0.0)
fastmap 1.0.1 2019-10-08 [1] CRAN (R 4.0.0)
fitdistrplus 1.1-1 2020-05-19 [1] CRAN (R 4.0.0)
flexmix 2.3-15 2019-02-18 [1] CRAN (R 4.0.0)
forcats * 0.5.0 2020-03-01 [1] CRAN (R 4.0.0)
foreach 1.5.0 2020-03-30 [1] CRAN (R 4.0.0)
foreign 0.8-80 2020-05-24 [1] CRAN (R 4.0.0)
fpc 2.2-7 2020-06-26 [1] CRAN (R 4.0.0)
fs 1.4.1 2020-04-04 [1] CRAN (R 4.0.0)
future 1.17.0 2020-04-18 [1] CRAN (R 4.0.0)
future.apply 1.5.0 2020-04-17 [1] CRAN (R 4.0.0)
gdata 2.18.0 2017-06-06 [1] CRAN (R 4.0.0)
generics 0.0.2 2018-11-29 [1] CRAN (R 4.0.0)
GenomeInfoDb * 1.24.2 2020-06-15 [1] Bioconductor
GenomeInfoDbData 1.2.3 2020-06-08 [1] Bioconductor
GenomicRanges * 1.40.0 2020-04-27 [1] Bioconductor
ggalluvial 0.11.3 2020-04-16 [1] CRAN (R 4.0.0)
ggplot2 * 3.3.2 2020-06-19 [1] CRAN (R 4.0.0)
ggpubr 0.4.0 2020-06-27 [1] CRAN (R 4.0.0)
ggrepel 0.8.2 2020-03-08 [1] CRAN (R 4.0.0)
ggridges 0.5.2 2020-01-12 [1] CRAN (R 4.0.0)
ggseqlogo 0.1 2017-07-25 [1] CRAN (R 4.0.0)
ggsignif 0.6.0 2019-08-08 [1] CRAN (R 4.0.0)
GlobalOptions 0.1.2 2020-06-10 [1] CRAN (R 4.0.0)
globals 0.12.5 2019-12-07 [1] CRAN (R 4.0.0)
glue 1.4.1 2020-05-13 [1] CRAN (R 4.0.0)
gplots 3.0.3 2020-02-25 [1] CRAN (R 4.0.0)
gridExtra 2.3 2017-09-09 [1] CRAN (R 4.0.0)
gsubfn 0.7 2018-03-16 [1] CRAN (R 4.0.0)
gtable 0.3.0 2019-03-25 [1] CRAN (R 4.0.0)
gtools 3.8.2 2020-03-31 [1] CRAN (R 4.0.0)
hash 2.2.6.1 2019-03-04 [1] CRAN (R 4.0.0)
haven 2.3.1 2020-06-01 [1] CRAN (R 4.0.0)
hcabm40k.SeuratData * 3.0.0 2020-06-25 [1] local
hms 0.5.3 2020-01-08 [1] CRAN (R 4.0.0)
htmltools 0.5.0 2020-06-16 [1] CRAN (R 4.0.0)
htmlwidgets 1.5.1 2019-10-08 [1] CRAN (R 4.0.0)
httpuv 1.5.4 2020-06-06 [1] CRAN (R 4.0.0)
httr 1.4.1 2019-08-05 [1] CRAN (R 4.0.0)
ica 1.0-2 2018-05-24 [1] CRAN (R 4.0.0)
igraph 1.2.5 2020-03-19 [1] CRAN (R 4.0.0)
immunarch * 0.6.5 2020-06-14 [1] CRAN (R 4.0.0)
interactiveDisplayBase 1.26.3 2020-06-02 [1] Bioconductor
IRanges * 2.22.2 2020-05-21 [1] Bioconductor
irlba 2.3.3 2019-02-05 [1] CRAN (R 4.0.0)
iterators 1.0.12 2019-07-26 [1] CRAN (R 4.0.0)
jsonlite 1.7.0 2020-06-25 [1] CRAN (R 4.0.0)
kernlab 0.9-29 2019-11-12 [1] CRAN (R 4.0.0)
KernSmooth 2.23-17 2020-04-26 [1] CRAN (R 4.0.0)
labeling 0.3 2014-08-23 [1] CRAN (R 4.0.0)
later 1.1.0.1 2020-06-05 [1] CRAN (R 4.0.0)
lattice 0.20-41 2020-04-02 [1] CRAN (R 4.0.0)
lazyeval 0.2.2 2019-03-15 [1] CRAN (R 4.0.0)
leiden 0.3.3 2020-02-04 [1] CRAN (R 4.0.0)
leidenbase 0.1.0 2020-06-08 [1] Github (cole-trapnell-lab/leidenbase@c22a7d0)
lifecycle 0.2.0 2020-03-06 [1] CRAN (R 4.0.0)
listenv 0.8.0 2019-12-05 [1] CRAN (R 4.0.0)
lmtest 0.9-37 2019-04-30 [1] CRAN (R 4.0.0)
lubridate 1.7.9 2020-06-08 [1] CRAN (R 4.0.0)
magrittr * 1.5 2014-11-22 [1] CRAN (R 4.0.0)
MASS 7.3-51.6 2020-04-26 [1] CRAN (R 4.0.0)
Matrix 1.2-18 2019-11-27 [1] CRAN (R 4.0.0)
matrixStats * 0.56.0 2020-03-13 [1] CRAN (R 4.0.0)
mclust 5.4.6 2020-04-11 [1] CRAN (R 4.0.0)
memoise 1.1.0 2017-04-21 [1] CRAN (R 4.0.0)
mime 0.9 2020-02-04 [1] CRAN (R 4.0.0)
modelr 0.1.8 2020-05-19 [1] CRAN (R 4.0.0)
modeltools 0.2-23 2020-03-05 [1] CRAN (R 4.0.0)
monocle3 * 0.2.2 2020-06-18 [1] Github (cole-trapnell-lab/monocle3@4137e48)
munsell 0.5.0 2018-06-12 [1] CRAN (R 4.0.0)
nlme 3.1-148 2020-05-24 [1] CRAN (R 4.0.0)
nnet 7.3-14 2020-04-26 [1] CRAN (R 4.0.0)
openxlsx 4.1.5 2020-05-06 [1] CRAN (R 4.0.0)
patchwork * 1.0.1.9000 2020-06-25 [1] Github (thomasp85/patchwork@82a5e03)
pbapply 1.4-2 2019-08-31 [1] CRAN (R 4.0.0)
pheatmap 1.0.12 2019-01-04 [1] CRAN (R 4.0.0)
pillar 1.4.4 2020-05-05 [1] CRAN (R 4.0.0)
pkgbuild 1.0.8 2020-05-07 [1] CRAN (R 4.0.0)
pkgconfig 2.0.3 2019-09-22 [1] CRAN (R 4.0.0)
pkgload 1.1.0 2020-05-29 [1] CRAN (R 4.0.0)
plotly 4.9.2.1 2020-04-04 [1] CRAN (R 4.0.0)
plotrix 3.7-8 2020-04-16 [1] CRAN (R 4.0.0)
plyr 1.8.6 2020-03-03 [1] CRAN (R 4.0.0)
png 0.1-7 2013-12-03 [1] CRAN (R 4.0.0)
prabclus 2.3-2 2020-01-08 [1] CRAN (R 4.0.0)
prettyunits 1.1.1 2020-01-24 [1] CRAN (R 4.0.0)
processx 3.4.2 2020-02-09 [1] CRAN (R 4.0.0)
promises 1.1.1 2020-06-09 [1] CRAN (R 4.0.0)
proto 1.0.0 2016-10-29 [1] CRAN (R 4.0.0)
proxy 0.4-24 2020-04-25 [1] CRAN (R 4.0.0)
proxyC 0.1.5 2019-07-21 [1] CRAN (R 4.0.0)
ps 1.3.3 2020-05-08 [1] CRAN (R 4.0.0)
purrr * 0.3.4 2020-04-17 [1] CRAN (R 4.0.0)
R6 2.4.1 2019-11-12 [1] CRAN (R 4.0.0)
RANN 2.6.1 2019-01-08 [1] CRAN (R 4.0.0)
rappdirs 0.3.1 2016-03-28 [1] CRAN (R 4.0.0)
RColorBrewer 1.1-2 2014-12-07 [1] CRAN (R 4.0.0)
Rcpp 1.0.4.6 2020-04-09 [1] CRAN (R 4.0.0)
RcppAnnoy 0.0.16 2020-03-08 [1] CRAN (R 4.0.0)
V RcppParallel 5.0.1 2020-06-24 [1] CRAN (R 4.0.0)
RCurl 1.98-1.2 2020-04-18 [1] CRAN (R 4.0.0)
readr * 1.3.1 2018-12-21 [1] CRAN (R 4.0.0)
readxl 1.3.1 2019-03-13 [1] CRAN (R 4.0.0)
remotes 2.1.1 2020-02-15 [1] CRAN (R 4.0.0)
reprex 0.3.0 2019-05-16 [1] CRAN (R 4.0.0)
reshape2 1.4.4 2020-04-09 [1] CRAN (R 4.0.0)
reticulate 1.16 2020-05-27 [1] CRAN (R 4.0.0)
rio 0.5.16 2018-11-26 [1] CRAN (R 4.0.0)
rlang 0.4.6 2020-05-02 [1] CRAN (R 4.0.0)
robustbase 0.93-6 2020-03-23 [1] CRAN (R 4.0.0)
ROCR 1.0-11 2020-05-02 [1] CRAN (R 4.0.0)
rprojroot 1.3-2 2018-01-03 [1] CRAN (R 4.0.0)
RSpectra 0.16-0 2019-12-01 [1] CRAN (R 4.0.0)
RSQLite 2.2.0 2020-01-07 [1] CRAN (R 4.0.0)
rstatix 0.6.0 2020-06-18 [1] CRAN (R 4.0.0)
rstudioapi 0.11 2020-02-07 [1] CRAN (R 4.0.0)
rsvd 1.0.3 2020-02-17 [1] CRAN (R 4.0.0)
Rtsne 0.15 2018-11-10 [1] CRAN (R 4.0.0)
rvest 0.3.5 2019-11-08 [1] CRAN (R 4.0.0)
S4Vectors * 0.26.1 2020-05-16 [1] Bioconductor
scales 1.1.1 2020-05-11 [1] CRAN (R 4.0.0)
scCATCH * 2.0 2020-06-05 [1] Github (ZJUFanLab/scCATCH@f7dec76)
V scTalk * 0.1.0 2020-06-30 [1] Github (VCCRI/scTalk@9af7dd2)
sctransform 0.2.1 2019-12-17 [1] CRAN (R 4.0.0)
sessioninfo 1.1.1 2018-11-05 [1] CRAN (R 4.0.0)
Seurat * 3.1.5 2020-04-16 [1] CRAN (R 4.0.0)
SeuratData * 0.2.1 2020-06-08 [1] Github (satijalab/seurat-data@12c77a8)
shape 1.4.4 2018-02-07 [1] CRAN (R 4.0.0)
V shiny * 1.4.0.2 2020-06-23 [1] CRAN (R 4.0.0)
shinythemes 1.1.2 2018-11-06 [1] CRAN (R 4.0.0)
SingleCellExperiment * 1.10.1 2020-04-28 [1] Bioconductor
SingleR * 1.2.4 2020-05-25 [1] Bioconductor
sqldf 0.4-11 2017-06-28 [1] CRAN (R 4.0.0)
STRINGdb * 2.0.1 2020-06-23 [1] Bioconductor
stringi * 1.4.6 2020-02-17 [1] CRAN (R 4.0.0)
stringr * 1.4.0 2019-02-10 [1] CRAN (R 4.0.0)
stxBrain.SeuratData * 0.1.1 2020-06-08 [1] local
SummarizedExperiment * 1.18.1 2020-04-30 [1] Bioconductor
survival 3.2-3 2020-06-13 [1] CRAN (R 4.0.0)
testthat 2.3.2 2020-03-02 [1] CRAN (R 4.0.0)
tibble * 3.0.1 2020-04-20 [1] CRAN (R 4.0.0)
tidyr * 1.1.0 2020-05-20 [1] CRAN (R 4.0.0)
tidyselect 1.1.0 2020-05-11 [1] CRAN (R 4.0.0)
tidyverse * 1.3.0 2019-11-21 [1] CRAN (R 4.0.0)
tsne 0.1-3 2016-07-15 [1] CRAN (R 4.0.0)
UpSetR 1.4.0 2019-05-22 [1] CRAN (R 4.0.0)
usethis * 1.6.1 2020-04-29 [1] CRAN (R 4.0.0)
uwot 0.1.8 2020-03-16 [1] CRAN (R 4.0.0)
vctrs 0.3.1 2020-06-05 [1] CRAN (R 4.0.0)
viridis 0.5.1 2018-03-29 [1] CRAN (R 4.0.0)
viridisLite 0.3.0 2018-02-01 [1] CRAN (R 4.0.0)
withr 2.2.0 2020-04-20 [1] CRAN (R 4.0.0)
xml2 1.3.2 2020-04-23 [1] CRAN (R 4.0.0)
xtable 1.8-4 2019-04-21 [1] CRAN (R 4.0.0)
XVector 0.28.0 2020-04-27 [1] Bioconductor
yaml 2.2.1 2020-02-01 [1] CRAN (R 4.0.0)
zip 2.0.4 2019-09-01 [1] CRAN (R 4.0.0)
zlibbioc 1.34.0 2020-04-27 [1] Bioconductor
zoo 1.8-8 2020-05-02 [1] CRAN (R 4.0.0)
[1] /Library/Frameworks/R.framework/Versions/4.0/Resources/library
V ── Loaded and on-disk version mismatch.Hi Wei,
Actually I also got an error using R v4 with the latest version of STRINGdb, although it was a different error. Can you confirm you got the same error as initially? It looks like a bug on the STRINGdb side, unfortunately, in the case where the STRING version is not supplied. However, if the STRING version is specified, in my case at least, it worked. Trying specifying string.ver = 11.0 in the GenerateEdgeWeights function and see if that works for you:
GenerateEdgeWeights(seurat.object = stanford,
file.label = file.lab, # output file
species = "human",
populations.use = populations.use,
string.ver = 11.0)Hi Ralph,
Yes, its the same error I got from the beginning. I just re-installed scTALK. I just reinstalled scTALK and ran the same command as you suggested, but now getting a different error :(
> GenerateEdgeWeights(seurat.object = stanford,
+ file.label = file.lab, # output file
+ species = "human",
+ populations.use = populations.use,
+ string.ver = 11.0) # this is a bug, need to run this line
[1] "Calculating cluster-specific ligand/expression characteristics"
[1] "Identifying all potential cluster:ligand:receptor:cluster paths"
Error: invalid assignment for reference class field ‘version’, should be from class “character” or a subclass (was class “numeric”)Very strange!
rj-patrick
commented
4 years ago Hi Wei,
Apologies, the STRING version should be a character. I.e. try the following:
GenerateEdgeWeights(seurat.object = stanford,
file.label = file.lab, # output file
species = "human",
populations.use = populations.use,
string.ver = "11.0")Hi Ralph,
Thank you so much again for troubleshooting with me! I changed the string.ver to "11.0" and now encounters a different error.
> GenerateEdgeWeights(seurat.object = stanford,
+ file.label = file.lab, # output file
+ species = "human",
+ populations.use = populations.use,
+ string.ver = "11.0") # this is a bug, need to run this line
[1] "Calculating cluster-specific ligand/expression characteristics"
[1] "Identifying all potential cluster:ligand:receptor:cluster paths"
Warning: we couldn't map to STRING 1% of your identifiersError in `.rowNamesDF<-`(x, value = value) :
duplicate 'row.names' are not allowed
In addition: Warning message:
non-unique value when setting 'row.names': ‘10090.ENSMUSP00000069114’
I am not sure where this row name comes from, it doesnt seem to follow the formats of anything in the RNA@data
rj-patrick
commented
4 years ago Hi Wei,
No worries, thanks for persevering! The identifier comes from STRING, and the error seems to relate to mapping gene symbols and STRING identifiers. I've added an extra check for duplicates, which should fix the issue (unless it's within STRINGdb). Please try reinstalling and run again. Also, try running with verbose = TRUE, which will print out additional run information if another issue comes up. I.e. the bellow command:
GenerateEdgeWeights(seurat.object = stanford,
file.label = file.lab, # output file
species = "human",
populations.use = populations.use,
string.ver = "11.0",
verbose = TRUE)Of course! I wished this would be a little smoother :) I am new to the scRNA field so I am also just learning as I go.
I have updated scTalk and ran the same script. Here is what I see;
> GenerateEdgeWeights(seurat.object = stanford,
+ file.label = file.lab, # output file
+ species = "human",
+ populations.use = populations.use,
+ string.ver = "11.0",
+ verbose = TRUE) # this is a bug, need to run this line
[1] "Calculating cluster-specific ligand/expression characteristics"
[1] "Identifying all potential cluster:ligand:receptor:cluster paths"
[1] "16885 potential paths in data. Some examples:"
Cluster1 Gene1 Gene1.Ave_Log2_exp Gene1.Log2_fold_change Gene1.Pct_expressed
1 0 A2M 2.990423 0.8502045 0.8628679
2 0 A2M 2.990423 0.8502045 0.8628679
3 0 A2M 2.990423 0.8502045 0.8628679
4 0 A2M 2.990423 0.8502045 0.8628679
5 0 A2M 2.990423 0.8502045 0.8628679
6 0 A2M 2.990423 0.8502045 0.8628679
Cluster2 Gene2 Gene2.Ave_Log2_exp Gene2.Log2_fold_change Gene2.Pct_expressed
1 1 LRP1 2.4014510 1.744605392 0.7461440
2 2 LRP1 1.1129596 -0.001806333 0.3936170
3 4 LRP1 1.5460357 0.477656285 0.5000000
4 5 LRP1 0.4100915 -0.742773700 0.1018809
5 6 LRP1 0.7396914 -0.396392623 0.2533113
6 8 LRP1 0.1046217 -1.046474148 0.1094737
[1] "216 ligands to score in STRING"
[1] "209 receptors score in STRING"
[1] "Connecting to STRING..."
[1] "Getting STRING identifier map"
[1] "Identifier map retrieved"
[1] "425 STRING results retrieved. Some examples:"
Gene Class STRING_id
9606.ENSP00000323929 A2M ligand 9606.ENSP00000323929
9606.ENSP00000260408 ADAM10 ligand 9606.ENSP00000260408
9606.ENSP00000349436 ADAM15 ligand 9606.ENSP00000349436
9606.ENSP00000309968 ADAM17 ligand 9606.ENSP00000309968
9606.ENSP00000264377 ADAM23 ligand 9606.ENSP00000264377
9606.ENSP00000265769 ADAM28 ligand 9606.ENSP00000265769
This graph was created by an old(er) igraph version.
Call upgrade_graph() on it to use with the current igraph version
For now we convert it on the fly...
Error in vcount(graph) :
REAL() can only be applied to a 'numeric', not a 'NULL'looks like i can go a little further now, but still error down the line.
rj-patrick
commented
4 years ago Hi Wei,
Thanks for running that. The problem seems to be occurring with STRINGdb but I'm unable to replicate the error myself. As a workaround, I've packaged the ligand-receptor STRING scores with scTalk, which will be used by default and circumvent this whole issue. If you reinstall, you should be able to run it now.
Cheers,
Ralph
wfma
commented
4 years ago fantastic, the latest update solved the issue! Thank you again Ralph! Wei
Hello!
I have a preprocessed Seurat object that I passed into GenerateEdgeWeights(). Here is my code:
Where 'stanford' is my seurat object. However, I am receiving this following output:
I am not sure how to proceed, could you please advise? Thank you! Wei