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hms-dbmi / scde

R package for analyzing single-cell RNA-seq data
http://pklab.med.harvard.edu/scde
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scde bioconductor version 2.10.0 still has flexmix problem! #76

Open tanpuekai opened 5 years ago

tanpuekai commented 5 years ago

Hi,

I mentioned in #73 that after several attempts i still have the flexmix problems, which remains unaddressed up to this day.

I noticed that you have made some updates on biodonductor page [https://www.bioconductor.org/packages/release/bioc/html/scde.html]. I happened to have a new PC with me in completely new and clean environment (Win10).

I installed R3.5.1, and then run your installation scripts:

if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install("scde", version = "3.8") For older versions of R, please refer to the appropriate Bioco

The installation run smoothly, and after that I was able to load scde. Below are the sessionInfo:

R version 3.5.1 (2018-07-02) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 10 x64 (build 17134)

Matrix products: default

locale: [1] LC_COLLATE=English_United States.1252 [2] LC_CTYPE=English_United States.1252
[3] LC_MONETARY=English_United States.1252 [4] LC_NUMERIC=C
[5] LC_TIME=English_United States.1252

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

other attached packages: [1] scde_2.10.0 flexmix_2.3-14 lattice_0.20-35

loaded via a namespace (and not attached): [1] zip_1.0.0 Rcpp_1.0.0
[3] cellranger_1.1.0 pillar_1.3.0
[5] compiler_3.5.1 RColorBrewer_1.1-2
[7] BiocManager_1.30.4 forcats_0.3.0
[9] tools_3.5.1 Lmoments_1.2-3
[11] tibble_1.4.2 nlme_3.1-137
[13] mgcv_1.8-24 pkgconfig_2.0.2
[15] rlang_0.3.0.1 openxlsx_4.1.0
[17] Matrix_1.2-14 curl_3.2
[19] parallel_3.5.1 SparseM_1.77
[21] haven_1.1.2 RcppArmadillo_0.9.200.4.0 [23] rio_0.5.10 extRemes_2.0-9
[25] MatrixModels_0.4-1 hms_0.4.2
[27] locfit_1.5-9.1 stats4_3.5.1
[29] grid_3.5.1 nnet_7.3-12
[31] Biobase_2.42.0 data.table_1.11.8
[33] distillery_1.0-4 Rook_1.1-1
[35] readxl_1.1.0 BiocParallel_1.16.0
[37] foreign_0.8-70 carData_3.0-2
[39] limma_3.38.2 car_3.0-2
[41] edgeR_3.24.0 magrittr_1.5
[43] pcaMethods_1.74.0 modeltools_0.2-22
[45] MASS_7.3-50 BiocGenerics_0.28.0
[47] abind_1.4-5 RMTstat_0.3
[49] brew_1.0-6 quantreg_5.36
[51] crayon_1.3.4 rjson_0.2.20
[53] Cairo_1.5-9

I then went on to run very simple scripts:

knn <- knn.error.models(cd.in, k = K, n.cores = NUMCORE, min.count.threshold = 1, min.nonfailed = 2, max.model.plots = 10, verbose=1)

And I immediately got these errors:

adjusting library size based on 2000 entries cell : calculating cell-cell similarities ... done fitting cell models: cell.1 : SRR7887424 Classification: weighted Error in FUN(X[[i]], ...) : trying to get slot "logLik" from an object of a basic class ("function") with no slots cell.2 : SRR7887425 Classification: weighted

At which point I stopped the program.

Would you pls help me by looking into this?

Best Chan

tanpuekai commented 5 years ago

OK, so I just realized that the 'flexmix' version is 2.3-14, which I know was causing many problems for me and for others, and I knew that in #40 you already have a solution. So I follow that solution:

library(devtools) install_version("flexmix", version = "2.3-13", repos = "http://cran.us.r-project.org") library(scde)

And below are the new sessionInfo:

R version 3.5.1 (2018-07-02) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 10 x64 (build 17134)

Matrix products: default

locale: [1] LC_COLLATE=English_United States.1252 [2] LC_CTYPE=English_United States.1252
[3] LC_MONETARY=English_United States.1252 [4] LC_NUMERIC=C
[5] LC_TIME=English_United States.1252

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

other attached packages: [1] scde_2.10.0 flexmix_2.3-13 lattice_0.20-35 usethis_1.4.0
[5] devtools_2.0.1

loaded via a namespace (and not attached): [1] Rcpp_1.0.0 locfit_1.5-9.1
[3] prettyunits_1.0.2 ps_1.2.1
[5] assertthat_0.2.0 rprojroot_1.3-2
[7] digest_0.6.18 R6_2.3.0
[9] cellranger_1.1.0 backports_1.1.2
[11] MatrixModels_0.4-1 stats4_3.5.1
[13] pillar_1.3.0 rlang_0.3.0.1
[15] curl_3.2 readxl_1.1.0
[17] data.table_1.11.8 SparseM_1.77
[19] car_3.0-2 callr_3.0.0
[21] Matrix_1.2-14 desc_1.2.0
[23] BiocParallel_1.16.0 foreign_0.8-70
[25] RMTstat_0.3 distillery_1.0-4
[27] compiler_3.5.1 pkgconfig_2.0.2
[29] extRemes_2.0-9 BiocGenerics_0.28.0
[31] base64enc_0.1-3 pkgbuild_1.0.2
[33] mgcv_1.8-24 pcaMethods_1.74.0
[35] nnet_7.3-12 tibble_1.4.2
[37] edgeR_3.24.0 Lmoments_1.2-3
[39] rio_0.5.10 crayon_1.3.4
[41] withr_2.1.2 MASS_7.3-50
[43] grid_3.5.1 nlme_3.1-137
[45] magrittr_1.5 zip_1.0.0
[47] cli_1.0.1 carData_3.0-2
[49] fs_1.2.6 RcppArmadillo_0.9.200.4.0 [51] remotes_2.0.2 limma_3.38.2
[53] brew_1.0-6 openxlsx_4.1.0
[55] rjson_0.2.20 RColorBrewer_1.1-2
[57] tools_3.5.1 Cairo_1.5-9
[59] forcats_0.3.0 Biobase_2.42.0
[61] glue_1.3.0 Rook_1.1-1
[63] hms_0.4.2 processx_3.2.0
[65] abind_1.4-5 pkgload_1.0.2
[67] parallel_3.5.1 sessioninfo_1.1.1
[69] memoise_1.1.0 haven_1.1.2
[71] quantreg_5.36 modeltools_0.2-22

So I then ran my old scripts, and still have the flexmix problems:

adjusting library size based on 2000 entries cell : calculating cell-cell similarities ... done fitting cell models: cell.1 : SRR7887424 Error in checkSlotAssignment(object, name, value) : assignment of an object of class “expression” is not valid for slot ‘defineComponent’ in an object of class “FLXMRglmC”; is(value, "expressionOrfunction") is not TRUE cell.2 : SRR7887425 Error in checkSlotAssignment(object, name, value) : assignment of an object of class “expression” is not valid for slot ‘defineComponent’ in an object of class “FLXMRglmC”; is(value, "expressionOrfunction") is not TRUE cell.3 : SRR7887426

Painful experience using your software. Pls help. Thanks!

pkharchenko commented 5 years ago

The proper way of addressing this is to move to an internal EM implementation (away from flex mix), and unfortunately we haven’t had anyone around the lab who could spend a couple of days on this so far. -peter.

On Nov 23, 2018, at 3:41 AM, CHEN Peikai notifications@github.com wrote:

OK, so I just realized that the 'flexmix' version is 2.3-14, which I know was causing many problems for me and for others, and I knew that in #40 https://github.com/hms-dbmi/scde/issues/40 you already have a solution. So I follow that solution:

library(devtools) install_version("flexmix", version = "2.3-13", repos = "http://cran.us.r-project.org http://cran.us.r-project.org/") library(scde)

And below are the new sessionInfo:

R version 3.5.1 (2018-07-02) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 10 x64 (build 17134)

Matrix products: default

locale: [1] LC_COLLATE=English_United States.1252 [2] LC_CTYPE=English_United States.1252 [3] LC_MONETARY=English_United States.1252 [4] LC_NUMERIC=C [5] LC_TIME=English_United States.1252

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

other attached packages: [1] scde_2.10.0 flexmix_2.3-13 lattice_0.20-35 usethis_1.4.0 [5] devtools_2.0.1

loaded via a namespace (and not attached): [1] Rcpp_1.0.0 locfit_1.5-9.1 [3] prettyunits_1.0.2 ps_1.2.1 [5] assertthat_0.2.0 rprojroot_1.3-2 [7] digest_0.6.18 R6_2.3.0 [9] cellranger_1.1.0 backports_1.1.2 [11] MatrixModels_0.4-1 stats4_3.5.1 [13] pillar_1.3.0 rlang_0.3.0.1 [15] curl_3.2 readxl_1.1.0 [17] data.table_1.11.8 SparseM_1.77 [19] car_3.0-2 callr_3.0.0 [21] Matrix_1.2-14 desc_1.2.0 [23] BiocParallel_1.16.0 foreign_0.8-70 [25] RMTstat_0.3 distillery_1.0-4 [27] compiler_3.5.1 pkgconfig_2.0.2 [29] extRemes_2.0-9 BiocGenerics_0.28.0 [31] base64enc_0.1-3 pkgbuild_1.0.2 [33] mgcv_1.8-24 pcaMethods_1.74.0 [35] nnet_7.3-12 tibble_1.4.2 [37] edgeR_3.24.0 Lmoments_1.2-3 [39] rio_0.5.10 crayon_1.3.4 [41] withr_2.1.2 MASS_7.3-50 [43] grid_3.5.1 nlme_3.1-137 [45] magrittr_1.5 zip_1.0.0 [47] cli_1.0.1 carData_3.0-2 [49] fs_1.2.6 RcppArmadillo_0.9.200.4.0 [51] remotes_2.0.2 limma_3.38.2 [53] brew_1.0-6 openxlsx_4.1.0 [55] rjson_0.2.20 RColorBrewer_1.1-2 [57] tools_3.5.1 Cairo_1.5-9 [59] forcats_0.3.0 Biobase_2.42.0 [61] glue_1.3.0 Rook_1.1-1 [63] hms_0.4.2 processx_3.2.0 [65] abind_1.4-5 pkgload_1.0.2 [67] parallel_3.5.1 sessioninfo_1.1.1 [69] memoise_1.1.0 haven_1.1.2 [71] quantreg_5.36 modeltools_0.2-22

So I then ran my old scripts, and still have the flexmix problems:

adjusting library size based on 2000 entries cell : calculating cell-cell similarities ... done fitting cell models: cell.1 : SRR7887424 Error in checkSlotAssignment(object, name, value) : assignment of an object of class “expression” is not valid for slot ‘defineComponent’ in an object of class “FLXMRglmC”; is(value, "expressionOrfunction") is not TRUE cell.2 : SRR7887425 Error in checkSlotAssignment(object, name, value) : assignment of an object of class “expression” is not valid for slot ‘defineComponent’ in an object of class “FLXMRglmC”; is(value, "expressionOrfunction") is not TRUE cell.3 : SRR7887426

Painful experience using your software. Pls help. Thanks!

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