Comments (4)
Hi @davemcg, I know a reproducible example is hard in this case, but could you give us some more information about the exact line of code you ran to get this error, the exact size of your datasets, and your session info?
We've successfully used scaleNotCenter on objects of up to 900k cells on machines with less than 500G of RAM.
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318 mb R list of two sparse matrides
# bash
wget https://hpc.nih.gov/~mcgaugheyd/test_data.Rdata .
# R
library(liger)
load('test_data.Rdata')
ligerex <- createLiger(test_data)
ligerex = normalize(ligerex)
ligerex = selectGenes(ligerex, var.thresh = 0.1, do.plot = FALSE)
ligerex <- scaleNotCenter(ligerex)
Error in asMethod(object) :
Cholmod error 'problem too large' at file ../Core/cholmod_dense.c, line 105
sessionInfo()
R version 3.6.0 (2019-04-26)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)
Matrix products: default
BLAS/LAPACK: /usr/local/intel/compilers_and_libraries_2019.1.144/linux/mkl/lib/intel64_lin/libmkl_rt.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] forcats_0.4.0 stringr_1.4.0 dplyr_0.8.3 purrr_0.3.2
[5] readr_1.3.1 tidyr_0.8.3 tibble_2.1.3 tidyverse_1.2.1
[9] liger_0.4.2 patchwork_0.0.1 Matrix_1.2-17 cowplot_0.9.4
[13] ggplot2_3.2.0
loaded via a namespace (and not attached):
[1] tidyselect_0.2.5 ica_1.0-2 RANN.L1_2.5.2 haven_2.1.0
[5] lattice_0.20-38 vctrs_0.2.0 colorspace_1.4-1 generics_0.0.2
[9] doSNOW_1.0.16 snow_0.4-3 utf8_1.1.4 rlang_0.4.0
[13] pillar_1.4.2 glue_1.3.1 withr_2.1.2 readxl_1.3.1
[17] modelr_0.1.4 foreach_1.4.4 plyr_1.8.4 cellranger_1.1.0
[21] munsell_0.5.0 gtable_0.3.0 rvest_0.3.4 codetools_0.2-16
[25] riverplot_0.6 irlba_2.3.3 parallel_3.6.0 fansi_0.4.0
[29] broom_0.5.2 Rcpp_1.0.1 scales_1.0.0 backports_1.1.4
[33] jsonlite_1.6 FNN_1.1.3 hms_0.4.2 stringi_1.4.3
[37] Rtsne_0.15 ggrepel_0.8.1 grid_3.6.0 cli_1.1.0
[41] tools_3.6.0 magrittr_1.5 lazyeval_0.2.2 zeallot_0.1.0
[45] crayon_1.3.4 pkgconfig_2.0.2 xml2_1.2.0 lubridate_1.7.4
[49] rstudioapi_0.10 assertthat_0.2.1 httr_1.4.0 iterators_1.0.10
[53] R6_2.4.0 mclust_5.4.3 nlme_3.1-140 compiler_3.6.0
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If I split the "big" matrix into two pieces (~40k and 140k) liger runs properly
from liger.
scaleNotCenter
works:
ligerex <- createLiger(list('A' = test_data$SRP158081[,1:150000], 'B' = test_data$SRP186407))
from liger.
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