emptyDrops result is full NAs
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Last seen 18 months ago

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] rhdf5
2.26.2 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

scran dropletUtils scater scRNA-Seq • 780 views
Entering edit mode

To list a few problems with your post:

  1. You don't show the code of the emptyDrops() call.
  2. You don't show the code leading up to the emptyDrops() call.
  3. You don't show the code that demonstrates that your "results is full of NAs".
  4. You're using an out-of-date installation of R and Bioconductor.

For comparison, see a good question here.


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