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jzitovsky / Analysis-Code-for-Zitovsky-and-Love-2019

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error running computationalResults.Rmd #2

Open stephens999 opened 4 years ago

stephens999 commented 4 years ago

I'm having some trouble running the code in this file.

I get an error at line 391: 

fit.mle <- apeglm(Y=y, x=x, log.lik=NULL, param=param, no.shrink=TRUE, log.link=FALSE, method = "betabinC")
Error in size[nonzero, , drop = FALSE] : incorrect number of dimensions

this is on the first time through the loop (i=2).

Here is some additional info:

> dim(y)
[1]   1 100
> dim(x)
[1] 100   2
> dim(param)
[1]   1 101

Any ideas?

Here is my sessionInfo: 

> sessionInfo()
R version 3.6.0 (2019-04-26)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS Mojave 10.14.4

Matrix products: default
BLAS:   /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.6/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] stats4    parallel  splines   stats     graphics  grDevices utils     datasets  methods  
[10] base     

other attached packages:
 [1] dichromat_2.0-0             microbenchmark_1.4-7        forcats_0.4.0              
 [4] stringr_1.4.0               dplyr_0.8.3                 purrr_0.3.3                
 [7] readr_1.3.1                 tidyr_1.0.0                 tibble_2.1.3               
[10] ggplot2_3.2.1               tidyverse_1.3.0             aods3_0.4-1.1              
[13] lme4_1.1-21                 Matrix_1.2-18               boot_1.3-23                
[16] VGAM_1.1-2                  ashr_2.2-39                 apeglm_1.8.0               
[19] DESeq2_1.26.0               airway_1.6.0                SummarizedExperiment_1.16.0
[22] DelayedArray_0.12.0         BiocParallel_1.20.0         matrixStats_0.55.0         
[25] Biobase_2.46.0              GenomicRanges_1.38.0        GenomeInfoDb_1.22.0        
[28] IRanges_2.20.1              S4Vectors_0.24.1            BiocGenerics_0.32.0        
[31] gamlss_5.1-5                nlme_3.1-142                gamlss.dist_5.1-5          
[34] MASS_7.3-51.4               gamlss.data_5.1-4           aod_1.3.1                  

loaded via a namespace (and not attached):
  [1] readxl_1.3.1           backports_1.1.5        Hmisc_4.3-0            plyr_1.8.4            
  [5] lazyeval_0.2.2         TH.data_1.0-10         digest_0.6.23          foreach_1.4.7         
  [9] htmltools_0.4.0        matrixcalc_1.0-3       SQUAREM_2017.10-1      fansi_0.4.0           
 [13] magrittr_1.5           checkmate_1.9.4        memoise_1.1.0          cluster_2.1.0         
 [17] doParallel_1.0.15      openxlsx_4.1.4         annotate_1.64.0        modelr_0.1.5          
 [21] sandwich_2.5-1         colorspace_1.4-1       blob_1.2.0             rvest_0.3.5           
 [25] haven_2.2.0            xfun_0.11              crayon_1.3.4           RCurl_1.95-4.12       
 [29] jsonlite_1.6           genefilter_1.68.0      zeallot_0.1.0          zoo_1.8-6             
 [33] survival_3.1-8         iterators_1.0.12       glue_1.3.1             gtable_0.3.0          
 [37] zlibbioc_1.32.0        XVector_0.26.0         car_3.0-5              abind_1.4-5           
 [41] scales_1.1.0           pscl_1.5.2             mvtnorm_1.0-11         DBI_1.0.0             
 [45] Rcpp_1.0.3             xtable_1.8-4           fmsb_0.6.3             emdbook_1.3.11        
 [49] htmlTable_1.13.3       foreign_0.8-72         bit_1.1-14             Formula_1.2-3         
 [53] truncnorm_1.0-8        htmlwidgets_1.5.1      httr_1.4.1             RColorBrewer_1.1-2    
 [57] acepack_1.4.1          farver_2.0.1           pkgconfig_2.0.3        XML_3.98-1.20         
 [61] nnet_7.3-12            dbplyr_1.4.2           locfit_1.5-9.1         labeling_0.3          
 [65] tidyselect_0.2.5       rlang_0.4.2            AnnotationDbi_1.48.0   munsell_0.5.0         
 [69] cellranger_1.1.0       tools_3.6.0            cli_2.0.0              generics_0.0.2        
 [73] RSQLite_2.1.4          broom_0.5.2            evaluate_0.14          HRQoL_1.0             
 [77] yaml_2.2.0             knitr_1.26             bit64_0.9-7            fs_1.3.1              
 [81] zip_2.0.4              rootSolve_1.8.1        xml2_1.2.2             compiler_3.6.0        
 [85] rstudioapi_0.10        curl_4.3               reprex_0.3.0           geneplotter_1.64.0    
 [89] stringi_1.4.3          lattice_0.20-38        nloptr_1.2.1           vctrs_0.2.0           
 [93] PROreg_1.0             pillar_1.4.2           lifecycle_0.1.0        cowplot_1.0.0         
 [97] data.table_1.12.8      bitops_1.0-6           R6_2.4.1               latticeExtra_0.6-28   
[101] gridExtra_2.3          rio_0.5.16             codetools_0.2-16       assertthat_0.2.1      
[105] withr_2.1.2            multcomp_1.4-10        GenomeInfoDbData_1.2.2 hms_0.5.2             
[109] grid_3.6.0             rpart_4.1-15           coda_0.19-3            minqa_1.2.4           
[113] rmarkdown_1.18         carData_3.0-3          mixsqp_0.2-8           bbmle_1.0.20          
[117] numDeriv_2016.8-1.1    lubridate_1.7.4        base64enc_0.1-3
jzitovsky commented 4 years ago

Dear stephens999,

Thank you for pointing this out. Its possible that the package we used for analysis is slightly different than the package we uploaded. I'm out of of town until early January. When I get back, I'll take a look and figure out what the issue is ASAP.

Josh