Running NMF for single cell
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@lirongrossmann-23954
Last seen 3.7 years ago

Hi,

I am trying to run NMF on my single cell matrix using scater package and it does not find the "runNMF". I also tried scater::runNMF and it did not work.

I used the following code:

BiocManager::install("scater")
library(scater)

Thanks

NMF scater • 2.0k views
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I find your lack of session information disturbing.

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Aaron is asking that you please include the output of sessionInfo() after loading the scater package. Here's mine:

> sessionInfo()
R version 4.0.2 Patched (2020-09-15 r79213)
Platform: x86_64-apple-darwin17.7.0 (64-bit)
Running under: macOS High Sierra 10.13.6

Matrix products: default
BLAS:   /Users/ma38727/bin/R-4-0-branch/lib/libRblas.dylib
LAPACK: /Users/ma38727/bin/R-4-0-branch/lib/libRlapack.dylib

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

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

other attached packages:
 [1] scater_1.16.2               ggplot2_3.3.2
 [3] SingleCellExperiment_1.10.1 SummarizedExperiment_1.18.2
 [5] DelayedArray_0.14.1         matrixStats_0.57.0
 [7] Biobase_2.48.0              GenomicRanges_1.40.0
 [9] GenomeInfoDb_1.24.2         IRanges_2.22.2
[11] S4Vectors_0.26.1            BiocGenerics_0.34.0

loaded via a namespace (and not attached):
 [1] Rcpp_1.0.5                vipor_0.4.5
 [3] compiler_4.0.2            pillar_1.4.6
 [5] XVector_0.28.0            viridis_0.5.1
 [7] DelayedMatrixStats_1.10.1 BiocNeighbors_1.6.0
 [9] bitops_1.0-6              tools_4.0.2
[11] zlibbioc_1.34.0           viridisLite_0.3.0
[13] lifecycle_0.2.0           tibble_3.0.3
[15] gtable_0.3.0              lattice_0.20-41
[17] pkgconfig_2.0.3           rlang_0.4.8
[19] Matrix_1.2-18             beeswarm_0.2.3
[21] gridExtra_2.3             GenomeInfoDbData_1.2.3
[23] withr_2.3.0               dplyr_1.0.2
[25] generics_0.0.2            vctrs_0.3.4
[27] grid_4.0.2                tidyselect_1.1.0
[29] glue_1.4.2                R6_2.4.1
[31] BiocParallel_1.22.0       ggbeeswarm_0.6.0
[33] irlba_2.3.3               BiocSingular_1.4.0
[35] purrr_0.3.4               magrittr_1.5
[37] scales_1.1.1              ellipsis_0.3.1
[39] rsvd_1.0.3                colorspace_1.4-1
[41] RCurl_1.98-1.2            munsell_0.5.0
[43] crayon_1.3.4

where you can see I'm using a current R (version 4.0.2) and scater (1.16.2). It's also helpful to see

> BiocManager::version()
[1] '3.11'

to confirm use of the current version of Bioconductor, and

> BiocManager::valid()
[1] TRUE

to show that my packages are all from the current version of Bioconductor.

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Thank you for your kind help! I think I was able to resolve it!

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Issue resolved. Don't be disturbed!

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Issue resolved. Don't be disturbed!

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