Closed galib36 closed 6 years ago
Hi,
What is you sessionInfo()
?
What happens if you run it like this?
sc3(sceObj, ks = 11, gene_filter = FALSE, biology = TRUE)
Cheers, Vlad
Hello Vlad, When I run the command you suggested get the same error.
In addition to the above mentioned error I also got the following warnings
Warning messages:
1: In as.POSIXlt.POSIXct(x, tz) :
unknown timezone 'zone/tz/2017c.1.0/zoneinfo/Europe/London'
2: package ‘registry’ was built under R version 3.4.3
Warning messages:
1: In as.POSIXlt.POSIXct(x, tz) :
unknown timezone 'zone/tz/2017c.1.0/zoneinfo/Europe/London'
2: package ‘registry’ was built under R version 3.4.3
Warning messages:
1: In as.POSIXlt.POSIXct(x, tz) :
unknown timezone 'zone/tz/2017c.1.0/zoneinfo/Europe/London'
2: package ‘registry’ was built under R version 3.4.3
I think, for the time zone it is not an issue but the Registry might be creating the problem?
The sessionInfo()
is as follows
R version 3.4.2 (2017-09-28)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS High Sierra 10.13.1
Matrix products: default
BLAS: /Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libRblas.0.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libRlapack.dylib
locale:
[1] en_GB.UTF-8/en_GB.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8
attached base packages:
[1] stats4 parallel stats graphics grDevices utils datasets
[8] methods base
other attached packages:
[1] SC3_1.6.0 scater_1.6.1
[3] SingleCellExperiment_1.0.0 SummarizedExperiment_1.8.0
[5] DelayedArray_0.4.1 matrixStats_0.52.2
[7] GenomicRanges_1.30.0 GenomeInfoDb_1.14.0
[9] IRanges_2.12.0 S4Vectors_0.16.0
[11] ggplot2_2.2.1 Biobase_2.38.0
[13] BiocGenerics_0.24.0
loaded via a namespace (and not attached):
[1] bitops_1.0-6 bit64_0.9-7 RColorBrewer_1.1-2
[4] doParallel_1.0.11 progress_1.1.2 dynamicTreeCut_1.63-1
[7] doRNG_1.6.6 tools_3.4.2 R6_2.2.2
[10] DT_0.2 KernSmooth_2.23-15 vipor_0.4.5
[13] DBI_0.7 lazyeval_0.2.1 colorspace_1.3-2
[16] gridExtra_2.3 prettyunits_1.0.2 bit_1.1-12
[19] compiler_3.4.2 pkgmaker_0.22 caTools_1.17.1
[22] scales_0.5.0 mvtnorm_1.0-6 DEoptimR_1.0-8
[25] robustbase_0.92-8 stringr_1.2.0 digest_0.6.12
[28] XVector_0.18.0 rrcov_1.4-3 pkgconfig_2.0.1
[31] htmltools_0.3.6 WriteXLS_4.0.0 limma_3.34.3
[34] htmlwidgets_0.9 rlang_0.1.4 RSQLite_2.0
[37] FNN_1.1 shiny_1.0.5 bindr_0.1
[40] zoo_1.8-0 BiocParallel_1.12.0 gtools_3.5.0
[43] dplyr_0.7.4 RCurl_1.95-4.8 magrittr_1.5
[46] GenomeInfoDbData_0.99.1 Matrix_1.2-12 Rcpp_0.12.14
[49] ggbeeswarm_0.6.0 munsell_0.4.3 viridis_0.4.0
[52] stringi_1.1.6 edgeR_3.20.1 zlibbioc_1.24.0
[55] rhdf5_2.22.0 gplots_3.0.1 plyr_1.8.4
[58] grid_3.4.2 blob_1.1.0 gdata_2.18.0
[61] shinydashboard_0.6.1 lattice_0.20-35 locfit_1.5-9.1
[64] igraph_1.1.2 rjson_0.2.15 rngtools_1.2.4
[67] codetools_0.2-15 reshape2_1.4.2 biomaRt_2.34.0
[70] XML_3.98-1.9 glue_1.2.0 scran_1.6.5
[73] data.table_1.10.4-3 foreach_1.4.3 httpuv_1.3.5
[76] gtable_0.2.0 assertthat_0.2.0 mime_0.5
[79] xtable_1.8-2 e1071_1.6-8 pcaPP_1.9-72
[82] class_7.3-14 viridisLite_0.2.0 pheatmap_1.0.8
[85] tibble_1.3.4 iterators_1.0.8 registry_0.5
[88] AnnotationDbi_1.40.0 beeswarm_0.2.3 memoise_1.1.0
[91] tximport_1.6.0 bindrcpp_0.2 cluster_2.0.6
[94] statmod_1.4.30 ROCR_1.0-7
Ok, can you share your sceObj
with me? (via e.g. Google Drive) vk6@sanger.ac.uk
Hello Vlad, I am sending you a zendto link with the .RDS file.
Best Regards, Syed
On 7 Dec 2017, at 17:04, Vladimir Kiselev notifications@github.com wrote:
Ok, can you share your sceObj with me? (via e.g. Google Drive) vk6@sanger.ac.uk mailto:vk6@sanger.ac.uk — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/hemberg-lab/SC3/issues/51#issuecomment-350031207, or mute the thread https://github.com/notifications/unsubscribe-auth/AJ96m2ZpMUohtD7ialPDRjdvRrM4x93lks5s-BqpgaJpZM4Q5vE1.
Hi, I found a problem. Somehow in your rowData
you had a column symbol
which was of data.frame
type. This is not good, SC3
assumes that all columns in the rowData
are of some simple type, e.g. numeric
, character
etc. So I removed this column and add a feature_symbol
column with gene names (it is required in the new version of SC3
- 1.7.2) and everything worked well:
library(SC3)
library(SingleCellExperiment)
d <- readRDS("~/Downloads/sceOBJ.rds")
rowData(d)$feature_symbol <- rownames(d)
# here I remove the symbol column
rowData(d) <- rowData(d)[,-1]
d <- sc3(d, ks = 11, biology = TRUE)
Let me know if it worked for you, Cheers, Vlad
Closing this assuming it was fixed
Hello, When I try to run
sc3(sceObj, ks = 11, biology = TRUE)
, it gives the following errorwhere I have 7635 genes in the
sceObj
Could you please let me know why the error and how to fix it?