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SketchData: Error in Calculating Leverage Score, fails with "NA/NaN/Inf in qr() function" error #9690

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nicholaslimwy opened this issue Feb 18, 2025 · 0 comments
Open

SketchData: Error in Calculating Leverage Score, fails with "NA/NaN/Inf in qr() function" error #9690

nicholaslimwy opened this issue Feb 18, 2025 · 0 comments

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@nicholaslimwy
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Hi! I've got a dataset of ~500k cells and was trying to use SketchData to scale my analysis. The dataset is a merged combination of 3 publicly available datasets of GEO + my own samples. Unfortunately everytime I try to run SketchData I run into the error "Calcuating Leverage Score
Error in qr.default(x = sa) : NA/NaN/Inf in foreign function call (arg 1)"

Here is my code:

finalpdc<-finalpdc<-merge(combatpdc,y=list(hivpdc,pdc,iavpdc))
finalpdc <- NormalizeData(finalpdc, normalization.method = "LogNormalize")
finalpdc <- FindVariableFeatures(finalpdc, verbose = F)
finalpdc <- SketchData(
  object = finalpdc,
  assay='RNA',
  ncells = 50000,
  method = "LeverageScore",
  sketched.assay = "sketch"
)

─ Session info ────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
 setting  value
 version  R version 4.3.0 (2023-04-21)
 os       Ubuntu 22.04.1 LTS
 system   x86_64, linux-gnu
 ui       RStudio
 language (EN)
 collate  en_US.UTF-8
 ctype    en_US.UTF-8
 tz       Etc/UTC
 date     2025-02-18
 rstudio  2023.03.0+386 Cherry Blossom (server)
 pandoc   2.19.2 @ /usr/lib/rstudio-server/bin/quarto/bin/tools/ (via rmarkdown)

─ Packages ────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
 package              * version    date (UTC) lib source
 abind                  1.4-5      2016-07-21 [1] RSPM (R 4.3.0)
 backports              1.4.1      2021-12-13 [1] RSPM (R 4.3.0)
 Biobase                2.60.0     2023-04-25 [1] Bioconductor
 BiocGenerics           0.46.0     2023-04-25 [1] Bioconductor
 BiocParallel           1.34.2     2023-05-22 [1] Bioconductor
 bitops                 1.0-7      2021-04-24 [1] RSPM (R 4.3.0)
 broom                  1.0.4      2023-03-11 [1] RSPM (R 4.3.0)
 cachem                 1.0.7      2023-02-24 [1] RSPM (R 4.3.0)
 callr                  3.7.3      2022-11-02 [1] RSPM (R 4.3.0)
 car                    3.1-3      2024-09-27 [1] RSPM (R 4.3.0)
 carData                3.0-5      2022-01-06 [1] RSPM (R 4.3.0)
 circlize               0.4.16     2024-02-20 [1] RSPM (R 4.3.0)
 cli                    3.6.1      2023-03-23 [1] RSPM (R 4.3.0)
 clue                   0.3-66     2024-11-13 [1] RSPM (R 4.3.0)
 cluster                2.1.4      2022-08-22 [2] CRAN (R 4.3.0)
 codetools              0.2-19     2023-02-01 [2] CRAN (R 4.3.0)
 colorspace             2.1-0      2023-01-23 [1] RSPM (R 4.3.0)
 ComplexHeatmap       * 2.16.0     2023-04-25 [1] Bioconductor
 cowplot              * 1.1.1      2020-12-30 [1] RSPM (R 4.3.0)
 crayon                 1.5.2      2022-09-29 [1] RSPM (R 4.3.0)
 data.table           * 1.14.8     2023-02-17 [1] RSPM (R 4.3.0)
 decoupleR            * 2.9.7      2025-02-18 [1] Github (saezlab/decoupleR@3a41229)
 DelayedArray           0.26.3     2023-05-22 [1] Bioconductor
 deldir                 1.0-6      2021-10-23 [1] RSPM (R 4.3.0)
 devtools               2.4.5      2022-10-11 [1] RSPM (R 4.3.0)
 digest                 0.6.31     2022-12-11 [1] RSPM (R 4.3.0)
 doParallel             1.0.17     2022-02-07 [1] RSPM (R 4.3.0)
 dotCall64              1.2        2024-10-04 [1] RSPM (R 4.3.0)
 dplyr                * 1.1.2      2023-04-20 [1] RSPM (R 4.3.0)
 ellipsis               0.3.2      2021-04-29 [1] RSPM (R 4.3.0)
 evaluate               0.20       2023-01-17 [1] RSPM (R 4.3.0)
 fansi                  1.0.4      2023-01-22 [1] RSPM (R 4.3.0)
 farver                 2.1.1      2022-07-06 [1] RSPM (R 4.3.0)
 fastDummies            1.7.5      2025-01-20 [1] RSPM (R 4.3.0)
 fastmap                1.1.1      2023-02-24 [1] RSPM (R 4.3.0)
 fastmatch              1.1-6      2024-12-23 [1] RSPM (R 4.3.0)
 fgsea                * 1.26.0     2023-04-25 [1] Bioconductor
 fitdistrplus           1.1-11     2023-04-25 [1] RSPM (R 4.3.0)
 forcats              * 1.0.0      2023-01-29 [1] RSPM (R 4.3.0)
 foreach                1.5.2      2022-02-02 [1] RSPM (R 4.3.0)
 Formula                1.2-5      2023-02-24 [1] RSPM (R 4.3.0)
 fs                     1.6.2      2023-04-25 [1] RSPM (R 4.3.0)
 future                 1.32.0     2023-03-07 [1] RSPM (R 4.3.0)
 future.apply           1.11.0     2023-05-21 [1] RSPM (R 4.3.0)
 generics               0.1.3      2022-07-05 [1] RSPM (R 4.3.0)
 GenomeInfoDb           1.36.0     2023-04-25 [1] Bioconductor
 GenomeInfoDbData       1.2.10     2023-05-16 [1] Bioconductor
 GenomicRanges          1.52.0     2023-04-25 [1] Bioconductor
 GetoptLong             1.0.5      2020-12-15 [1] RSPM (R 4.3.0)
 GGally               * 2.2.1      2024-02-14 [1] RSPM (R 4.3.0)
 ggfortify            * 0.4.17     2024-04-17 [1] RSPM (R 4.3.0)
 ggplot2              * 3.5.0      2024-02-23 [1] CRAN (R 4.3.0)
 ggpubr               * 0.6.0.999  2025-02-14 [1] Github (kassambara/ggpubr@6aeb4f7)
 ggrepel                0.9.3      2023-02-03 [1] RSPM (R 4.3.0)
 ggridges               0.5.4      2022-09-26 [1] RSPM (R 4.3.0)
 ggsignif               0.6.4      2022-10-13 [1] RSPM (R 4.3.0)
 ggstats                0.8.0      2025-01-07 [1] RSPM (R 4.3.0)
 glmGamPoi            * 1.12.2     2023-07-02 [1] Bioconductor
 GlobalOptions          0.1.2      2020-06-10 [1] RSPM (R 4.3.0)
 globals                0.16.2     2022-11-21 [1] RSPM (R 4.3.0)
 glue                   1.6.2      2022-02-24 [1] RSPM (R 4.3.0)
 goftest                1.2-3      2021-10-07 [1] RSPM (R 4.3.0)
 gridExtra              2.3        2017-09-09 [1] RSPM (R 4.3.0)
 gtable                 0.3.3      2023-03-21 [1] RSPM (R 4.3.0)
 harmony              * 1.2.3      2024-11-27 [1] RSPM (R 4.3.0)
 hms                    1.1.3      2023-03-21 [1] RSPM (R 4.3.0)
 htmltools              0.5.5      2023-03-23 [1] RSPM (R 4.3.0)
 htmlwidgets            1.6.2      2023-03-17 [1] RSPM (R 4.3.0)
 httpuv                 1.6.9      2023-02-14 [1] RSPM (R 4.3.0)
 httr                   1.4.6      2023-05-08 [1] RSPM (R 4.3.0)
 ica                    1.0-3      2022-07-08 [1] RSPM (R 4.3.0)
 igraph                 1.4.2      2023-04-07 [1] RSPM (R 4.3.0)
 IRanges                2.34.0     2023-04-25 [1] Bioconductor
 irlba                  2.3.5.1    2022-10-03 [1] RSPM (R 4.3.0)
 iterators              1.0.14     2022-02-05 [1] RSPM (R 4.3.0)
 jsonlite               1.8.4      2022-12-06 [1] RSPM (R 4.3.0)
 KernSmooth             2.23-20    2021-05-03 [2] CRAN (R 4.3.0)
 knitr                * 1.42       2023-01-25 [1] RSPM (R 4.3.0)
 later                  1.3.0      2021-08-18 [1] RSPM (R 4.3.0)
 lattice                0.21-8     2023-04-05 [2] CRAN (R 4.3.0)
 lazyeval               0.2.2      2019-03-15 [1] RSPM (R 4.3.0)
 lifecycle              1.0.3      2022-10-07 [1] RSPM (R 4.3.0)
 listenv                0.9.0      2022-12-16 [1] RSPM (R 4.3.0)
 lmtest                 0.9-40     2022-03-21 [1] RSPM (R 4.3.0)
 lubridate            * 1.9.2      2023-02-10 [1] RSPM (R 4.3.0)
 magrittr               2.0.3      2022-03-30 [1] RSPM (R 4.3.0)
 MASS                   7.3-59     2023-04-21 [2] RSPM (R 4.3.0)
 Matrix                 1.6-5      2024-01-11 [1] CRAN (R 4.3.0)
 MatrixGenerics         1.12.0     2023-04-25 [1] Bioconductor
 matrixStats            0.63.0     2022-11-18 [1] RSPM (R 4.3.0)
 memoise                2.0.1      2021-11-26 [1] RSPM (R 4.3.0)
 mime                   0.12       2021-09-28 [1] RSPM (R 4.3.0)
 miniUI                 0.1.1.1    2018-05-18 [1] RSPM (R 4.3.0)
 munsell                0.5.0      2018-06-12 [1] RSPM (R 4.3.0)
 nlme                   3.1-162    2023-01-31 [2] CRAN (R 4.3.0)
 openxlsx             * 4.2.8      2025-02-17 [1] Github (ycphs/openxlsx@9b094b9)
 parallelly             1.35.0     2023-03-23 [1] RSPM (R 4.3.0)
 patchwork              1.3.0.9000 2025-02-13 [1] Github (thomasp85/patchwork@2695a9f)
 pbapply                1.7-0      2023-01-13 [1] RSPM (R 4.3.0)
 pillar                 1.9.0      2023-03-22 [1] RSPM (R 4.3.0)
 pkgbuild               1.4.0      2022-11-27 [1] RSPM (R 4.3.0)
 pkgconfig              2.0.3      2019-09-22 [1] RSPM (R 4.3.0)
 pkgload                1.3.2      2022-11-16 [1] RSPM (R 4.3.0)
 plotly                 4.10.1     2022-11-07 [1] RSPM (R 4.3.0)
 plyr                   1.8.8      2022-11-11 [1] RSPM (R 4.3.0)
 png                    0.1-8      2022-11-29 [1] RSPM (R 4.3.0)
 PNWColors            * 0.1.0      2025-02-18 [1] Github (jakelawlor/PNWColors@f16a14f)
 polyclip               1.10-4     2022-10-20 [1] RSPM (R 4.3.0)
 presto               * 1.0.0      2025-02-05 [1] Github (immunogenomics/presto@7636b3d)
 prettyunits            1.1.1      2020-01-24 [1] RSPM (R 4.3.0)
 processx               3.8.1      2023-04-18 [1] RSPM (R 4.3.0)
 profvis                0.3.7      2020-11-02 [1] RSPM (R 4.3.0)
 progressr              0.13.0     2023-01-10 [1] RSPM (R 4.3.0)
 promises               1.2.0.1    2021-02-11 [1] RSPM (R 4.3.0)
 ps                     1.7.5      2023-04-18 [1] RSPM (R 4.3.0)
 purrr                * 1.0.1      2023-01-10 [1] RSPM (R 4.3.0)
 R6                     2.5.1      2021-08-19 [1] RSPM (R 4.3.0)
 RANN                   2.6.1      2019-01-08 [1] RSPM (R 4.3.0)
 RColorBrewer         * 1.1-3      2022-04-03 [1] RSPM (R 4.3.0)
 Rcpp                 * 1.0.10     2023-01-22 [1] RSPM (R 4.3.0)
 RcppAnnoy              0.0.20     2022-10-27 [1] RSPM (R 4.3.0)
 RcppHNSW               0.4.1      2022-07-18 [1] RSPM (R 4.3.0)
 RCurl                  1.98-1.12  2023-03-27 [1] RSPM (R 4.3.0)
 readr                * 2.1.4      2023-02-10 [1] RSPM (R 4.3.0)
 remotes                2.4.2      2021-11-30 [1] RSPM (R 4.3.0)
 reshape2             * 1.4.4      2020-04-09 [1] RSPM (R 4.3.0)
 reticulate             1.28       2023-01-27 [1] RSPM (R 4.3.0)
 rjson                  0.2.21     2022-01-09 [1] RSPM (R 4.3.0)
 rlang                  1.1.1      2023-04-28 [1] RSPM (R 4.3.0)
 rmarkdown              2.21       2023-03-26 [1] RSPM (R 4.3.0)
 ROCR                   1.0-11     2020-05-02 [1] RSPM (R 4.3.0)
 RSpectra               0.16-2     2024-07-18 [1] RSPM (R 4.3.0)
 rstatix                0.7.2      2023-02-01 [1] RSPM (R 4.3.0)
 rstudioapi             0.14       2022-08-22 [1] RSPM (R 4.3.0)
 rsvd                 * 1.0.5      2021-04-16 [1] RSPM (R 4.3.0)
 Rtsne                  0.16       2022-04-17 [1] RSPM (R 4.3.0)
 S4Arrays               1.0.4      2023-05-14 [1] Bioconductor
 S4Vectors              0.38.1     2023-05-02 [1] Bioconductor
 scales                 1.3.0      2023-11-28 [1] RSPM (R 4.3.0)
 scattermore            1.2        2023-06-12 [1] RSPM (R 4.3.0)
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 sessioninfo            1.2.2      2021-12-06 [1] RSPM (R 4.3.0)
 Seurat               * 5.2.1      2025-01-24 [1] RSPM (R 4.3.0)
 SeuratObject         * 5.0.2      2024-05-08 [1] RSPM (R 4.3.0)
 shape                  1.4.6.1    2024-02-23 [1] RSPM (R 4.3.0)
 shiny                  1.7.4      2022-12-15 [1] RSPM (R 4.3.0)
 sp                   * 1.6-0      2023-01-19 [1] RSPM (R 4.3.0)
 spam                   2.11-1     2025-01-20 [1] RSPM (R 4.3.0)
 spatstat.data          3.0-1      2023-03-12 [1] RSPM (R 4.3.0)
 spatstat.explore       3.1-0      2023-03-14 [1] RSPM (R 4.3.0)
 spatstat.geom          3.1-0      2023-03-12 [1] RSPM (R 4.3.0)
 spatstat.random        3.1-4      2023-03-13 [1] RSPM (R 4.3.0)
 spatstat.sparse        3.0-1      2023-03-12 [1] RSPM (R 4.3.0)
 spatstat.utils         3.1-2      2025-01-08 [1] RSPM (R 4.3.0)
 stringi                1.7.12     2023-01-11 [1] RSPM (R 4.3.0)
 stringr              * 1.5.0      2022-12-02 [1] RSPM (R 4.3.0)
 SummarizedExperiment   1.30.1     2023-05-01 [1] Bioconductor
 survival               3.5-5      2023-03-12 [2] CRAN (R 4.3.0)
 tensor                 1.5        2012-05-05 [1] RSPM (R 4.3.0)
 tibble               * 3.2.1      2023-03-20 [1] RSPM (R 4.3.0)
 tidyr                * 1.3.0      2023-01-24 [1] RSPM (R 4.3.0)
 tidyselect             1.2.0      2022-10-10 [1] RSPM (R 4.3.0)
 tidyverse            * 2.0.0      2023-02-22 [1] RSPM (R 4.3.0)
 timechange             0.2.0      2023-01-11 [1] RSPM (R 4.3.0)
 tzdb                   0.3.0      2022-03-28 [1] RSPM (R 4.3.0)
 urlchecker             1.0.1      2021-11-30 [1] RSPM (R 4.3.0)
 usethis                2.1.6      2022-05-25 [1] RSPM (R 4.3.0)
 utf8                   1.2.3      2023-01-31 [1] RSPM (R 4.3.0)
 uwot                   0.1.14     2022-08-22 [1] RSPM (R 4.3.0)
 vctrs                  0.6.2      2023-04-19 [1] RSPM (R 4.3.0)
 viridisLite            0.4.1      2022-08-22 [1] RSPM (R 4.3.0)
 withr                  2.5.0      2022-03-03 [1] RSPM (R 4.3.0)
 xfun                   0.39       2023-04-20 [1] RSPM (R 4.3.0)
 xtable                 1.8-4      2019-04-21 [1] RSPM (R 4.3.0)
 XVector                0.40.0     2023-04-25 [1] Bioconductor
 yaml                   2.3.7      2023-01-23 [1] RSPM (R 4.3.0)
 zip                    2.3.0      2023-04-17 [1] RSPM (R 4.3.0)
 zlibbioc               1.46.0     2023-04-25 [1] Bioconductor
 zoo                    1.8-12     2023-04-13 [1] RSPM (R 4.3.0)

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