doubletCluster error: invalid rownames length

[marionilab]

doubletCluster error: invalid rownames length

[LTLA]

Can you make a minimum reproducible example?

https://stackoverflow.com/questions/5963269/how-to-make-a-great-r-reproducible-example

Certainly I have no problems running doubletCluster on a SingleCellExperiment object:

https://bioconductor.org/packages/devel/workflows/vignettes/simpleSingleCell/inst/doc/work-6-doublet.html#3_doublet_detection_with_clusters

... which is probably where you got the code from anyway.

[danshu]

This seems to have something to do with rownames.
counts <- as.matrix(counts(sce))
rownames(counts) <- c()
dbl.out <- doubletCluster(counts, sce$Cluster)
After deleting rownames, there is no error now.

On the other hand, for the example (https://rdrr.io/github/MarioniLab/scran/man/doubletCluster.html):
rownames(counts) <- paste0("gene",1:100)
After giving rownames to "counts", I got the same error.

Interestingly, I got the same error when running "read10xCounts()". Actually, there is no such error before I updated scater and scran.

R version 3.5.1 (2018-07-02)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Debian GNU/Linux buster/sid

Matrix products: default
BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.8.0
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.8.0

locale:
[1] LC_CTYPE=en_HK.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_HK.UTF-8 LC_COLLATE=en_HK.UTF-8
[5] LC_MONETARY=en_HK.UTF-8 LC_MESSAGES=en_HK.UTF-8
[7] LC_PAPER=en_HK.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_HK.UTF-8 LC_IDENTIFICATION=C

attached base packages:
[1] parallel stats4 stats graphics grDevices utils datasets
[8] methods base

other attached packages:
[1] DropletUtils_1.0.3 SingleCellExperiment_1.3.11
[3] SummarizedExperiment_1.10.1 DelayedArray_0.7.48
[5] matrixStats_0.54.0 Biobase_2.40.0
[7] GenomicRanges_1.32.7 GenomeInfoDb_1.16.0
[9] IRanges_2.14.12 S4Vectors_0.19.22
[11] BiocGenerics_0.27.1 BiocParallel_1.14.2

loaded via a namespace (and not attached):
[1] Rcpp_0.12.19 XVector_0.20.0 edgeR_3.23.5
[4] lattice_0.20-35 tools_3.5.1 grid_3.5.1
[7] rhdf5_2.25.11 Matrix_1.2-14 GenomeInfoDbData_1.1.0
[10] Rhdf5lib_1.3.3 bitops_1.0-6 RCurl_1.95-4.11
[13] limma_3.36.5 compiler_3.5.1 locfit_1.5-9.1

[LTLA]

Regarding the modified example; I observe no such error with the following code:

library(scran)

# Mocking up an example.
ngenes <- 100
mu1 <- 2^rexp(ngenes)
mu2 <- 2^rnorm(ngenes)

counts.1 <- matrix(rpois(ngenes*100, mu1), nrow=ngenes)
counts.2 <- matrix(rpois(ngenes*100, mu2), nrow=ngenes)
counts.m <- matrix(rpois(ngenes*20, mu1+mu2), nrow=ngenes)

counts <- cbind(counts.1, counts.2, counts.m)
clusters <- rep(1:3, c(ncol(counts.1), ncol(counts.2), ncol(counts.m)))
rownames(counts) <- paste0("gene", seq_len(ngenes))

# Find potential doublets: works fine for me.
dbl <- doubletCluster(counts, clusters)

If you want to use the latest version of scran, then you should also be using the latest version of the other Bioconductor packages. I would suggest running BiocManager::install(version="devel") to synchronize the other packages; this may or may not solve your problem.

Session information

R version 3.5.0 RC (2018-04-16 r74624)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: OS X El Capitan 10.11.6

Matrix products: default
BLAS: /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRblas.0.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.5/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] parallel  stats4    stats     graphics  grDevices utils     datasets 
[8] methods   base     

other attached packages:
 [1] scran_1.9.36                SingleCellExperiment_1.3.11
 [3] SummarizedExperiment_1.11.6 DelayedArray_0.7.48        
 [5] matrixStats_0.54.0          Biobase_2.41.2             
 [7] GenomicRanges_1.33.14       GenomeInfoDb_1.17.2        
 [9] IRanges_2.15.18             S4Vectors_0.19.22          
[11] BiocGenerics_0.27.1         BiocParallel_1.15.15       

loaded via a namespace (and not attached):
 [1] statmod_1.4.30            beeswarm_0.2.3           
 [3] locfit_1.5-9.1            tidyselect_0.2.5         
 [5] reshape2_1.4.3            purrr_0.2.5              
 [7] HDF5Array_1.9.19          lattice_0.20-35          
 [9] rhdf5_2.25.11             colorspace_1.3-2         
[11] viridisLite_0.3.0         rlang_0.2.2              
[13] pillar_1.3.0              glue_1.3.0               
[15] bindrcpp_0.2.2            GenomeInfoDbData_1.2.0   
[17] plyr_1.8.4                bindr_0.1.1              
[19] stringr_1.3.1             zlibbioc_1.27.0          
[21] munsell_0.5.0             gtable_0.2.0             
[23] vipor_0.4.5               scater_1.9.21            
[25] BiocNeighbors_0.99.22     Rcpp_0.12.19             
[27] edgeR_3.23.5              scales_1.0.0             
[29] limma_3.37.7              XVector_0.21.4           
[31] gridExtra_2.3             ggplot2_3.0.0            
[33] stringi_1.2.4             dplyr_0.7.6              
[35] grid_3.5.0                tools_3.5.0              
[37] bitops_1.0-6              magrittr_1.5             
[39] RCurl_1.95-4.11           lazyeval_0.2.1           
[41] tibble_1.4.2              dynamicTreeCut_1.63-1    
[43] crayon_1.3.4              pkgconfig_2.0.2          
[45] Matrix_1.2-14             DelayedMatrixStats_1.3.11
[47] ggbeeswarm_0.6.0          assertthat_0.2.0         
[49] viridis_0.5.1             Rhdf5lib_1.3.3           
[51] R6_2.3.0                  igraph_1.2.2             
[53] compiler_3.5.0           

[danshu]

Thanks!
Updating "other attached packages" to development versions solved this problem.