Error when using results() in the script bladder-deseq.R

[ge2sasag]

Hi,

I'm using the bladder-deseq.R script and I'm stuck in this step:

deseq_results = results(dds, contrast=c("is_benefit", "True", "False"))

because it reports this error:

Error in if (!expanded & (hasIntercept | noInterceptPullCoef)) { : 
  argument is of length zero

Any ideas on how can I solve it?

Session info:

> sessionInfo()
R version 3.6.1 (2019-07-05)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 18362)

Matrix products: default

locale:
[1] LC_COLLATE=Spanish_Spain.1252  LC_CTYPE=Spanish_Spain.1252    LC_MONETARY=Spanish_Spain.1252 LC_NUMERIC=C                  
[5] LC_TIME=Spanish_Spain.1252    

attached base packages:
[1] parallel  stats4    stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] gageData_2.24.0             gage_2.36.0                 DESeq2_1.26.0               readr_1.3.1                
 [5] tximport_1.14.0             SummarizedExperiment_1.16.1 DelayedArray_0.12.2         BiocParallel_1.20.1        
 [9] matrixStats_0.55.0          Biobase_2.46.0              GenomicRanges_1.38.0        GenomeInfoDb_1.22.0        
[13] IRanges_2.20.2              S4Vectors_0.24.3            BiocGenerics_0.32.0        

loaded via a namespace (and not attached):
 [1] bitops_1.0-6           bit64_0.9-7            RColorBrewer_1.1-2     httr_1.4.1             tools_3.6.1           
 [6] backports_1.1.5        R6_2.4.1               rpart_4.1-15           Hmisc_4.3-0            DBI_1.1.0             
[11] lazyeval_0.2.2         colorspace_1.4-1       nnet_7.3-12            tidyselect_0.2.5       gridExtra_2.3         
[16] bit_1.1-15.1           compiler_3.6.1         graph_1.64.0           cli_2.0.1              htmlTable_1.13.3      
[21] scales_1.1.0           checkmate_1.9.4        genefilter_1.68.0      stringr_1.4.0          digest_0.6.23         
[26] foreign_0.8-71         XVector_0.26.0         base64enc_0.1-3        jpeg_0.1-8.1           pkgconfig_2.0.3       
[31] htmltools_0.4.0        htmlwidgets_1.5.1      rlang_0.4.4            rstudioapi_0.11        RSQLite_2.2.0         
[36] acepack_1.4.1          dplyr_0.8.4            RCurl_1.98-1.1         magrittr_1.5           GenomeInfoDbData_1.2.2
[41] Formula_1.2-3          Matrix_1.2-17          Rcpp_1.0.3             munsell_0.5.0          fansi_0.4.1           
[46] lifecycle_0.1.0        stringi_1.4.5          zlibbioc_1.32.0        grid_3.6.1             blob_1.2.1            
[51] crayon_1.3.4           lattice_0.20-38        Biostrings_2.54.0      splines_3.6.1          annotate_1.64.0       
[56] hms_0.5.3              KEGGREST_1.26.1        locfit_1.5-9.1         zeallot_0.1.0          knitr_1.28            
[61] pillar_1.4.3           geneplotter_1.64.0     XML_3.99-0.3           glue_1.3.1             latticeExtra_0.6-29   
[66] data.table_1.12.8      png_0.1-7              vctrs_0.2.1            gtable_0.3.0           purrr_0.3.3           
[71] assertthat_0.2.1       ggplot2_3.2.1          xfun_0.12              xtable_1.8-4           survival_3.1-8        
[76] tibble_2.1.3           AnnotationDbi_1.48.0   memoise_1.1.0          cluster_2.1.0         
>