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hemberg-lab / SC3

A tool for the unsupervised clustering of cells from single cell RNA-Seq experiments
http://bioconductor.org/packages/SC3
GNU General Public License v3.0
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sc3(s) giving error #51

Closed galib36 closed 6 years ago

galib36 commented 6 years ago

Hello, When I try to run sc3(sceObj, ks = 11, biology = TRUE), it gives the following error

Error in `[<-`(`*tmp*`, , paste0("sc3_", k, "_markers_clusts"), value = c(NA, : 7635 rows in value to replace 1 rows

where I have 7635 genes in the sceObj

Could you please let me know why the error and how to fix it?

wikiselev commented 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

galib36 commented 6 years ago

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
wikiselev commented 6 years ago

Ok, can you share your sceObj with me? (via e.g. Google Drive) vk6@sanger.ac.uk

galib36 commented 6 years ago

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.

wikiselev commented 6 years ago

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

wikiselev commented 6 years ago

Closing this assuming it was fixed