Last updated: 2019-12-04

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File Version Author Date Message
Rmd bdfa678 Matthew Stephens 2019-12-04 workflowr::wflow_publish(c(“ash_pois_bcell.Rmd”, “../data/b-cell-data.Rds”)) 
library("ashr")
library("ebpm")

Introduction

The goal here is to look at some examples where ash_pois may not fit the data well (data provided by A Sarkar).

Read in the data and extract data for first gene:

b_data= readRDS("../data/b-cell-data.Rds")
gene_names = unique(b_data$gene)
b_data1 = b_data[b_data$gene == gene_names[1],]
hist(b_data1$count/b_data1$size, main="observed expression values across cells")

Now fit ash and point gamma:

b1_ash = ash_pois(b_data1$count, b_data1$size)
b1_pg = ebpm_point_gamma(b_data1$count, b_data1$size)
Warning in (function (f, p, ..., hessian = FALSE, typsize = rep(1,
length(p)), : NA/Inf replaced by maximum positive value
b1_ash$loglik
[1] -31402.69
b1_pg$log_likelihood
[1] -31414.6

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:   /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRblas.0.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] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] ebpm_0.0.0.9003 ashr_2.2-39    

loaded via a namespace (and not attached):
 [1] Rcpp_1.0.3        knitr_1.23        whisker_0.3-2    
 [4] magrittr_1.5      workflowr_1.5.0   MASS_7.3-51.4    
 [7] pscl_1.5.2        doParallel_1.0.15 SQUAREM_2017.10-1
[10] lattice_0.20-38   R6_2.4.0          foreach_1.4.7    
[13] stringr_1.4.0     tools_3.6.0       parallel_3.6.0   
[16] grid_3.6.0        xfun_0.8          git2r_0.26.1     
[19] gtools_3.8.1      iterators_1.0.12  htmltools_0.3.6  
[22] yaml_2.2.0        digest_0.6.22     rprojroot_1.3-2  
[25] mixsqp_0.2-8      Matrix_1.2-17     later_0.8.0      
[28] codetools_0.2-16  promises_1.0.1    fs_1.3.1         
[31] glue_1.3.1        evaluate_0.14     rmarkdown_1.14   
[34] stringi_1.4.3     compiler_3.6.0    backports_1.1.5  
[37] truncnorm_1.0-8   httpuv_1.5.1