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View Code? Open in Web Editor NEWMarker gene selection from scRNA-seq data
Marker gene selection from scRNA-seq data
When using this nice package, I was confused by whether the input expression should be log or anti-log transformed.
The example data are log-transfromed.
data(melanoma)
melanoma1 = as.matrix(melanoma[, 2:dim(melanoma)[2]])
row.names(melanoma1) = melanoma[, 1]
range(melanoma1)
[1] 0.000 15.923
In SCcluster()
, NormalizeData()
from the Seurat
is called, and data are log-transformed again by normalization.method = "LogNormalize"
.
Then in getClusterGene()
, get_marker_genes()
from the SC3
package is called. According to its example, get_marker_genes()
takes in anti-log transformed data as input, other than the log-transformed data.
range(yan[1:10,])
[1] 0 9225
Dear authors of SCMarker,
I've been trying to run the tutorial with the GMB dataset, where Seurat and SCMarker are used together. However, they require different versions of R (Seurat works with 3.6.3 and SCMarker with 3.5.3). Are you planning to release an upgraded version of SCMarker that works with R 3.6.3? If yes, when?
Kind regards,
Elin
Hi there,
I'm quite keen to test out SCMarker; however, when I try to install it from github using devtools, it fails with the following error:
Error : (converted from warning) /tmp/RtmpqxidqW/R.INSTALL6a8b4f4b65c4/SCMarker/man/HeatmapCluster.Rd:86: unexpected END_OF_INPUT '}
'
ERROR: installing Rd objects failed for package ‘SCMarker’
* removing ‘/home/common/BioC/R-3.6.0-release_BioC-3.9-release/SCMarker’
Error: Failed to install 'SCMarker' from GitHub:
(converted from warning) installation of package ‘/tmp/RtmpGawVqT/file2f54df03bb4/SCMarker_2.0.tar.gz’ had non-zero exit status
Looks like a problem with some of the documentation? I also tried download the tar.gz source code, but I got the same error.
Thanks for the help!
Sarah
Dear Sir,
Can you please fix the issue I encountered in installing your package?
Cheers
Calogero
###########
I tried installing your package:
library(devtools)
Loading required package: usethis
install_github("KChen-lab/SCMarker")
Downloading GitHub repo KChen-lab/SCMarker@master
✔ checking for file ‘/private/var/folders/_b/4rmqysy94j91kb8xjyc551z40000gn/T/Rtmpgv8C6V/remotes15f6348ff42e/KChen-lab-SCMarker-c07d842/DESCRIPTION’ ...
─ preparing ‘SCMarker’:
✔ checking DESCRIPTION meta-information ...
Warning: /private/var/folders/_b/4rmqysy94j91kb8xjyc551z40000gn/T/RtmpeP6Kqc/Rbuild17d32bd5251d/SCMarker/man/HeatmapCluster.Rd:86: unexpected END_OF_INPUT '}
'
─ installing the package to process help pages
─ saving partial Rd database (1.3s)
─ checking for LF line-endings in source and make files and shell scripts
─ checking for empty or unneeded directories
─ looking to see if a ‘data/datalist’ file should be added
─ building ‘SCMarker_2.0.tar.gz’
I cloned the repository and I did a build test and I got the following issues:
warning 1
✔ checking DESCRIPTION meta-information ...
Warning: /private/var/folders/_b/4rmqysy94j91kb8xjyc551z40000gn/T/RtmpOtbfSW/Rbuild16401f1c0c3c/SCMarker/man/HeatmapCluster.Rd:86: unexpected END_OF_INPUT '}
error 1:
checking for unstated dependencies in examples ... WARNING
Warning: parse error in file 'SCMarker-Ex.R':
156:5: unexpected symbol
155: topmarker=as.data.frame(feature
156: topmarker
^
I was wondering if it is possible to use your package with embedding (integrated data), such as the output from Harmony.
If yes, could you explain how?
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