Hi Tom, I am writing to seek your help in using baySeq for DGE analysis of RNA-Seq data from 9 subjects at two points each. So, there are 18 samples in total with 9 pairs. I am trying to run the code below after looking at some of the answers you provided for previous queries and the documentation at: http://bioconductor.org/packages/release/bioc/vignettes/baySeq/inst/doc/baySeq_generic.pdf

However, I am getting an error in the getLikelihoods function with or without nullProps parameter :

> pairCD <- getLikelihoods(pairCD, pET = 'BIC', nullData = TRUE, cl = cl) #, nullProps=0.5)
**Error in rep(1, nrow(cD@priors$sampled)) : invalid 'times' argument**
> pairCD <- getLikelihoods(pairCD, pET = 'BIC', nullData = TRUE, cl = cl, nullProps=0.5)
**Error in getLikelihoods(pairCD, pET = "BIC", nullData = TRUE, cl = cl,  : 
  unused argument (nullProps = 0.5)**

Below is the code and the sessionInfo.

I really appreciate all the help.

Thanks Sharvari

pairCD <- new("countData", data = list(PooledCounts[,1:9], PooledCounts[,10:18]),
          replicates = as.factor(rep("A",9)),
          groups = list(Agroup = as.factor(rep("A",9))),
          densityFunction = bbDensity
          )

libsizes(pairCD) <- getLibsizes(pairCD)

#fit priors and calculate posterior likelihoods based on our specified distributional model
pairCD <- getPriors(pairCD, samplesize = 10000, cl = cl)
pairCD <- getLikelihoods(pairCD, pET = 'BIC', nullData = TRUE, cl = cl) #, nullProps=0.5)
out <- topCounts(pairCD, group = "Agroup")

sessionInfo( )
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Monterey 12.2

Matrix products: default
LAPACK: /Library/Frameworks/R.framework/Versions/4.1/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  stats4    stats     graphics  grDevices utils     datasets  methods  
[9] base     

other attached packages:
 [1] baySeq_2.28.0        abind_1.4-5          GenomicRanges_1.46.1 GenomeInfoDb_1.30.1 
 [5] umap_0.2.8.0         matrixStats_0.62.0   ggplot2_3.3.5        data.table_1.14.2   
 [9] statmod_1.4.36       gageData_2.32.0      gage_2.44.0          pathview_1.34.0     
[13] org.Hs.eg.db_3.14.0  AnnotationDbi_1.56.2 IRanges_2.28.0       S4Vectors_0.32.4    
[17] Biobase_2.54.0       BiocGenerics_0.40.0  BiocManager_1.30.17  stringr_1.4.0       
[21] edgeR_3.36.0         limma_3.50.3        

loaded via a namespace (and not attached):
 [1] bitops_1.0-7           bit64_4.0.5            httr_1.4.2            
 [4] Rgraphviz_2.38.0       tools_4.1.3            utf8_1.2.2            
 [7] R6_2.5.1               DT_0.22                DBI_1.1.2             
[10] colorspace_2.0-3       withr_2.5.0            tidyselect_1.1.2      
[13] bit_4.0.4              compiler_4.1.3         graph_1.72.0          
[16] textshaping_0.3.6      cli_3.3.0              labeling_0.4.2        
[19] KEGGgraph_1.54.0       scales_1.2.0           askpass_1.1           
[22] systemfonts_1.0.4      digest_0.6.29          XVector_0.34.0        
[25] pkgconfig_2.0.3        htmltools_0.5.2        fastmap_1.1.0         
[28] htmlwidgets_1.5.4      rlang_1.0.2            rstudioapi_0.13       
[31] RSQLite_2.2.12         generics_0.1.2         farver_2.1.0          
[34] jsonlite_1.8.0         dplyr_1.0.8            RCurl_1.98-1.6        
[37] magrittr_2.0.3         GO.db_3.14.0           GenomeInfoDbData_1.2.7
[40] Matrix_1.4-1           Rcpp_1.0.8.3           munsell_0.5.0         
[43] fansi_1.0.3            reticulate_1.24        lifecycle_1.0.1       
[46] stringi_1.7.6          zlibbioc_1.40.0        grid_4.1.3            
[49] blob_1.2.3             crayon_1.5.1           lattice_0.20-45       
[52] Biostrings_2.62.0      splines_4.1.3          KEGGREST_1.34.0       
[55] locfit_1.5-9.5         pillar_1.7.0           XML_3.99-0.9          
[58] glue_1.6.2             png_0.1-7              vctrs_0.4.1           
[61] gtable_0.3.0           openssl_2.0.0          purrr_0.3.4           
[64] assertthat_0.2.1       cachem_1.0.6           RSpectra_0.16-0       
[67] ragg_1.2.2             tibble_3.1.6           memoise_2.0.1         
[70] ellipsis_0.3.2        
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