Question: error running sc3_plot_de_genes in SC3 R package
0
gravatar for weiqiao1029
7 months ago by
weiqiao10290 wrote:

Hello, When I try to run sc3_plot_de_genes(sce, k = 4), it gives the following error

Error in seq.default(min(x, na.rm = T), max(x, na.rm = T), length.out = n +  : 
  'from' must be a finite number
In addition: Warning messages:
1: In min(x, na.rm = T) : no non-missing arguments to min; returning Inf
2: In max(x, na.rm = T) : no non-missing arguments to max; returning -Inf

and also in the following function sc3_plot_markers(sce, k = 4),it gives the following error

No markers have been found, try to lower significance thresholds!

but other function sc3_plot_expression(sce, k = 4),sc3_plot_consensus(sce, k = 4)seems worked, Could you please give me some advice about how to fix it? I am looking for the marker genes.

Thanks in advance,

sc3 • 157 views
ADD COMMENTlink modified 7 months ago by Vladimir Kiselev150 • written 7 months ago by weiqiao10290

And the sessionInfo()are as followings: sessionInfo() R version 3.5.2 (2018-12-20) Platform: x86_64-apple-darwin15.6.0 (64-bit) Running under: macOS High Sierra 10.13.1

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] scater1.10.1 ggplot23.1.0 SC31.10.1
[4] SingleCellExperiment
1.4.1 SummarizedExperiment1.12.0 DelayedArray0.8.0
[7] BiocParallel1.16.5 matrixStats0.54.0 Biobase2.42.0
[10] GenomicRanges
1.34.0 GenomeInfoDb1.18.1 IRanges2.16.0
[13] S4Vectors0.20.1 BiocGenerics0.28.0 loaded via a namespace (and not attached): [1] bitops1.0-6 doParallel1.0.14 RColorBrewer1.1-2
[4] tools
3.5.2 doRNG1.7.1 R62.3.0
[7] KernSmooth2.23-15 HDF5Array1.10.1 vipor0.4.5
[10] lazyeval
0.2.1 colorspace1.4-0 withr2.1.2
[13] tidyselect0.2.5 gridExtra2.3 compiler3.5.2
[16] pkgmaker
0.27 labeling0.3 caTools1.17.1.1
[19] scales1.0.0 DEoptimR1.0-8 mvtnorm1.0-8
[22] robustbase
0.93-3 stringr1.3.1 digest0.6.18
[25] XVector0.22.0 rrcov1.4-7 pkgconfig2.0.2
[28] htmltools
0.3.6 bibtex0.4.2 WriteXLS4.0.0
[31] rlang0.3.1 rstudioapi0.9.0 shiny1.2.0
[34] DelayedMatrixStats
1.4.0 bindr0.1.1 gtools3.8.1
[37] dplyr0.7.8 RCurl1.95-4.11 magrittr1.5
[40] GenomeInfoDbData
1.2.0 Matrix1.2-15 Rcpp1.0.0
[43] ggbeeswarm0.6.0 munsell0.5.0 Rhdf5lib1.4.2
[46] viridis
0.5.1 stringi1.2.4 yaml2.2.0
[49] zlibbioc1.28.0 rhdf52.26.2 gplots3.0.1
[52] plyr
1.8.4 grid3.5.2 gdata2.18.0
[55] promises1.0.1 crayon1.3.4 lattice0.20-38
[58] cowplot
0.9.4 pillar1.3.1 rngtools1.3.1
[61] reshape21.4.3 codetools0.2-15 glue1.3.0
[64] httpuv
1.4.5.1 foreach1.4.4 gtable0.2.0
[67] purrr0.2.5 assertthat0.2.0 mime0.6
[70] xtable
1.8-3 e10711.7-0 later0.7.5
[73] class7.3-14 pcaPP1.9-73 viridisLite0.3.0
[76] tibble
2.0.1 pheatmap1.0.12 iterators1.0.10
[79] registry0.5 beeswarm0.2.3 bindrcpp0.2.2
[82] cluster
2.0.7-1 ROCR_1.0-7

ADD REPLYlink written 7 months ago by weiqiao10290
Answer: error running sc3_plot_de_genes in SC3 R package
0
gravatar for Vladimir Kiselev
7 months ago by
Sanger Institute, Cambridge, UK
Vladimir Kiselev150 wrote:

I've replied on GitHub: https://github.com/hemberg-lab/SC3/issues/88#issuecomment-465484299

ADD COMMENTlink written 7 months ago by Vladimir Kiselev150
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