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"Error in if (tol * ans$d[1] < eps) warning("convergence criterion below machine epsilon") : missing value where TRUE/FALSE needed" #54
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Hi!
Sorry you ran into trouble, it does look
like a bug :(.
I'm looking in to this and will let you know as soon as i have a workaround
for you.
…On Mon, Jul 6, 2020 at 3:05 PM Neerja Katiyar ***@***.***> wrote:
Hi, I am trying to integrate scRNA-seq and scATAC-seq data using Seurat's
vignette ((
https://satijalab.org/seurat/v3.1/atacseq_integration_vignette.html)
The following step is giving me an error.
pbmc.atac <- RunUMAP(pbmc.atac, reduction = "lsi", dims = 1:50).
Here is the error.
"Error in if (tol * ans$d[1] < eps) warning("convergence criterion below machine epsilon") :
missing value where TRUE/FALSE needed"?
> sessionInfo()
R version 3.6.1 (2019-07-05)
Platform: x86_64-conda_cos6-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)
Matrix products: default
BLAS/LAPACK: /home/katiyn/miniconda3/lib/R/lib/libRblas.so
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] patchwork_1.0.0 ggplot2_3.3.0 Seurat_3.1.5
loaded via a namespace (and not attached):
[1] rsvd_1.0.3 ggrepel_0.8.2 Rcpp_1.0.4.6
[4] ape_5.3 lattice_0.20-38 ica_1.0-2
[7] tidyr_1.0.3 listenv_0.8.0 png_0.1-7
[10] zoo_1.8-8 assertthat_0.2.1 digest_0.6.25
[13] lmtest_0.9-37 R6_2.4.1 plyr_1.8.6
[16] ggridges_0.5.2 httr_1.4.1 pillar_1.4.4
[19] rlang_0.4.6 lazyeval_0.2.2 data.table_1.12.8
[22] irlba_2.3.3 leiden_0.3.3 Matrix_1.2-17
[25] reticulate_1.15 splines_3.6.1 Rtsne_0.15
[28] stringr_1.4.0 htmlwidgets_1.5.1 uwot_0.1.8
[31] igraph_1.2.5 munsell_0.5.0 sctransform_0.2.1
[34] compiler_3.6.1 pkgconfig_2.0.3 globals_0.12.5
[37] htmltools_0.4.0 tidyselect_1.1.0 gridExtra_2.3
[40] tibble_3.0.1 RANN_2.6.1 codetools_0.2-16
[43] fitdistrplus_1.0-14 future_1.17.0 viridisLite_0.3.0
[46] withr_2.2.0 crayon_1.3.4 dplyr_0.8.5
[49] MASS_7.3-51.3 rappdirs_0.3.1 grid_3.6.1
[52] tsne_0.1-3 nlme_3.1-139 jsonlite_1.6.1
[55] gtable_0.3.0 lifecycle_0.2.0 magrittr_1.5
[58] npsurv_0.4-0.1 scales_1.1.1 KernSmooth_2.23-15
[61] stringi_1.4.6 future.apply_1.5.0 lsei_1.2-0.1
[64] pbapply_1.4-2 reshape2_1.4.4 ROCR_1.0-11
[67] ellipsis_0.3.0 vctrs_0.3.0 cowplot_1.0.0
[70] RcppAnnoy_0.0.16 RColorBrewer_1.1-2 tools_3.6.1
[73] glue_1.4.0 purrr_0.3.4 parallel_3.6.1
[76] survival_3.1-12 colorspace_1.4-1 cluster_2.0.8
[79] plotly_4.9.2.1
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I got the same error with a different dataset. In my case it was caused by some -Inf values in the input data. After removing those values all was fine. |
the same error. Firstly I ran irlba on a dataset and the error didn't occur. Then I got the same error when I ran irlba on subset of the dataset. There's no -inf values. The package version is 2.3.5. Any solution? |
There is a minor change on the current GitHub version you can try; it probably does not address the root cause but it might help. If someone can share a reproducible example with me, it would help... |
Hi, I am trying to integrate scRNA-seq and scATAC-seq data using Seurat's vignette ((https://satijalab.org/seurat/v3.1/atacseq_integration_vignette.html)
The following step is giving me an error.
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