Hello, I am trying to use emptyDrops function of dropletUtils package. I used it on my raw counts data but the results is full of NAs. How can I solve this problem or what can be wrong about my data?
Thank you in advance.
My sessionInfo:
R version 3.5.2 (2018-12-20) Platform: x86_64-apple-darwin15.6.0 (64-bit) Running under: macOS High Sierra 10.13.2
Matrix products: default BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib LAPACK: /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRlapack.dylib
locale: [1] enUS.UTF-8/enUS.UTF-8/enUS.UTF-8/C/enUS.UTF-8/en_US.UTF-8
attached base packages: [1] parallel stats4 stats graphics grDevices utils datasets methods base
other attached packages:
[1] DropletUtils1.2.2 SingleCellExperiment1.4.1 SummarizedExperiment1.12.0 DelayedArray0.8.0 matrixStats0.54.0 Biobase2.42.0
[7] GenomicRanges1.34.0 GenomeInfoDb1.18.2 IRanges2.16.0 S4Vectors0.20.1 BiocGenerics0.28.0 BiocParallel1.16.6
loaded via a namespace (and not attached):
[1] Rcpp1.0.1 edgeR3.24.3 XVector0.22.0 zlibbioc1.28.0 lattice0.20-38 tools3.5.2 grid3.5.2
[8] rhdf52.26.2 HDF5Array1.10.1 yaml2.2.0 Matrix1.2-17 GenomeInfoDbData1.2.0 Rhdf5lib1.4.3 bitops1.0-6
[15] RCurl1.95-4.12 limma3.38.3 compiler3.5.2 locfit1.5-9.1
To list a few problems with your post:
emptyDrops()
call.emptyDrops()
call.For comparison, see a good question here.