scde bioconductor version 2.10.0 still has flexmix problem!

[tanpuekai]

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]

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]

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 ***@***.***> 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 <#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! — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#76 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/ALT78tYdtqIdPr5yH6LQKF0mFR9CMCkrks5ux7ShgaJpZM4YwQG0>.