Error in building scde.error.models
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efe...@broadinstitute.org
May 24, 2017, 8:36:09 PM5/24/17
to SCDE
Hi,
I previously had the error solved in a previous topic, which was solved by going back to an old version of flexmix.
After that the errors changed to:
o.ifm <- scde.error.models(counts = cd, groups = sg, n.cores = 1, threshold.segmentation = TRUE, save.crossfit.plots = FALSE, save.model.plots = FALSE, verbose = 1)
cross-fitting cells.
number of pairs: 190
number of pairs: 190
total number of pairs: 380
cross-fitting 380 pairs:
building individual error models.
adjusting library size based on 2000 entries
fitting ESC models:
1 : ESC_10
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
2 : ESC_11
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
I used the data(es.mef.small) included with the scde package (get the same error with own data)
> sessionInfo()
R version 3.4.0 (2017-04-21)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS Sierra 10.12.3
Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libRlapack.dylib
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] parallel stats graphics grDevices utils datasets methods
[8] base
other attached packages:
[1] RColorBrewer_1.1-2 RANN_2.5.1 gmodels_2.16.2
[4] tidyr_0.6.3 scde_2.4.1 scater_1.4.0
[7] Biobase_2.36.2 BiocGenerics_0.22.0 useful_1.2.1
[10] dplyr_0.5.0 Matrix_1.2-10 ggplot2_2.2.1
[13] biomaRt_2.32.0 flexmix_2.3-13 lattice_0.20-35
loaded via a namespace (and not attached):
[1] nlme_3.1-131 bitops_1.0-6
[3] matrixStats_0.52.2 pbkrtest_0.4-7
[5] tools_3.4.0 backports_1.1.0
[7] R6_2.2.1 rpart_4.1-11
[9] vipor_0.4.5 Hmisc_4.0-3
[11] DBI_0.6-1 lazyeval_0.2.0
[13] mgcv_1.8-17 colorspace_1.3-2
[15] nnet_7.3-12 gridExtra_2.2.1
[17] compiler_3.4.0 quantreg_5.33
[19] htmlTable_1.9 Cairo_1.5-9
[21] SparseM_1.77 sandwich_2.3-4
[23] tcltk2_1.2-11 scales_0.4.1
[25] checkmate_1.8.2 RcmdrMisc_1.0-5
[27] Lmoments_1.2-3 stringr_1.2.0
[29] digest_0.6.12 foreign_0.8-68
[31] relimp_1.0-5 minqa_1.2.4
[33] distillery_1.0-2 base64enc_0.1-3
[35] htmltools_0.3.6 Rcmdr_2.3-2
[37] lme4_1.1-13 extRemes_2.0-8
[39] limma_3.32.2 htmlwidgets_0.8
[41] rlang_0.1.1 readxl_1.0.0
[43] RSQLite_1.1-2 shiny_1.0.3
[45] zoo_1.8-0 gtools_3.5.0
[47] BiocParallel_1.10.1 acepack_1.4.1
[49] car_2.1-4 RCurl_1.95-4.8
[51] magrittr_1.5 modeltools_0.2-21
[53] Formula_1.2-1 Rcpp_0.12.11
[55] ggbeeswarm_0.5.3 munsell_0.4.3
[57] S4Vectors_0.14.1 abind_1.4-5
[59] viridis_0.4.0 stringi_1.1.5
[61] edgeR_3.18.1 MASS_7.3-47
[63] zlibbioc_1.22.0 rhdf5_2.20.0
[65] plyr_1.8.4 grid_3.4.0
[67] gdata_2.17.0 shinydashboard_0.6.0
[69] splines_3.4.0 locfit_1.5-9.1
[71] knitr_1.16 tcltk_3.4.0
[73] rjson_0.2.15 reshape2_1.4.2
[75] stats4_3.4.0 XML_3.98-1.7
[77] RcppArmadillo_0.7.800.2.0 latticeExtra_0.6-28
[79] pcaMethods_1.68.0 data.table_1.10.4
[81] nloptr_1.0.4 httpuv_1.3.3
[83] MatrixModels_0.4-1 cellranger_1.1.0
[85] RMTstat_0.3 gtable_0.2.0
[87] assertthat_0.2.0 mime_0.5
[89] xtable_1.8-2 e1071_1.6-8
[91] class_7.3-14 survival_2.41-3
[93] viridisLite_0.2.0 tibble_1.3.1
[95] AnnotationDbi_1.38.0 beeswarm_0.2.3
[97] memoise_1.1.0 IRanges_2.10.1
[99] Rook_1.1-1 tximport_1.4.0
[101] cluster_2.0.6 brew_1.0-6
Thank you in advance for any help!
efe...@broadinstitute.org
May 25, 2017, 1:26:39 PM5/25/17
to SCDE
Hi!
I just seem to have solved the problem by installing the latest development version of "scde" 1.99.4. I left flexmix as 2-3.13 and restarted R. I have not tried my own data yet, but the dataset provided with the package works fine now.
Installed development version of scde from GitHub as mentioned on the website:
require(devtools)
devtools::install_github('hms-dbmi/scde', build_vignettes = FALSE)Message has been deleted
杨璐
Nov 2, 2017, 9:29:14 PM11/2/17
to SCDE
I have the same problem, but it was not solved by reinstall the scde.
> sessionInfo()
R version 3.4.2 (2017-09-28)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows >= 8 x64 (build 9200)
Matrix products: default
locale:
[1] LC_COLLATE=Chinese (Simplified)_China.936 LC_CTYPE=Chinese (Simplified)_China.936
[3] LC_MONETARY=Chinese (Simplified)_China.936 LC_NUMERIC=C
[5] LC_TIME=Chinese (Simplified)_China.936
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] scde_1.99.4 flexmix_2.3-13 lattice_0.20-35
loaded via a namespace (and not attached):
[1] Rcpp_0.12.13 edgeR_3.18.1 splines_3.4.2 BiocGenerics_0.22.1
[5] MASS_7.3-47 BiocParallel_1.10.1 rjson_0.2.15 brew_1.0-6
[9] RcppArmadillo_0.8.100.1.0 minqa_1.2.4 distillery_1.0-4 car_2.1-5
[13] Rook_1.1-1 Lmoments_1.2-3 tools_3.4.2 pbkrtest_0.4-7
[17] nnet_7.3-12 parallel_3.4.2 RMTstat_0.3 grid_3.4.2
[21] Biobase_2.36.2 nlme_3.1-131 mgcv_1.8-22 quantreg_5.34
[25] modeltools_0.2-21 MatrixModels_0.4-1 lme4_1.1-14 Matrix_1.2-11
[29] nloptr_1.0.4 RColorBrewer_1.1-2 extRemes_2.0-8 limma_3.32.10
[33] compiler_3.4.2 pcaMethods_1.68.0 stats4_3.4.2 locfit_1.5-9.1
[37] SparseM_1.77 Cairo_1.5-9
Pierre Migeon
Nov 4, 2017, 4:11:42 PM11/4/17
to SCDE
I also continue to have issues with both running with scde_1.99.4 and flexmix_2.3-13
Matthew Sapio
Nov 10, 2017, 10:32:58 AM11/10/17
to SCDE
Yes I also have many problems with the package. Right now it says:
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
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