For the sake of reproducibility, here’s a list of packages and their versions that were used to create this R markdown document.

devtools::session_info()
 setting  value                       
 version  R version 3.3.0 (2016-05-03)
 system   x86_64, darwin13.4.0        
 ui       X11                         
 language (EN)                        
 collate  en_CA.UTF-8                 
 tz       America/Vancouver           
 date     2016-11-09                  

 package              * version    date       source                        
 acepack                1.4.0      2016-10-20 CRAN (R 3.3.0)                
 annotate               1.50.1     2016-10-09 Bioconductor                  
 AnnotationDbi          1.34.4     2016-07-08 Bioconductor                  
 assertthat             0.1        2013-12-06 CRAN (R 3.3.0)                
 Biobase                2.32.0     2016-05-04 Bioconductor                  
 BiocGenerics           0.18.0     2016-05-04 Bioconductor                  
 BiocParallel           1.6.6      2016-08-15 Bioconductor                  
 biomaRt                2.28.0     2016-05-05 Bioconductor                  
 bitops                 1.0-6      2013-08-17 CRAN (R 3.3.0)                
 car                    2.1-3      2016-08-11 CRAN (R 3.3.0)                
 caret                * 6.0-71     2016-08-05 CRAN (R 3.3.0)                
 chron                  2.3-47     2015-06-24 CRAN (R 3.3.0)                
 class                  7.3-14     2015-08-30 CRAN (R 3.3.0)                
 cluster                2.0.5      2016-10-08 CRAN (R 3.3.0)                
 codetools              0.2-15     2016-10-05 CRAN (R 3.3.0)                
 colorspace             1.2-7      2016-10-11 CRAN (R 3.3.0)                
 cowplot                0.6.3      2016-09-30 CRAN (R 3.3.0)                
 crayon                 1.3.2      2016-06-28 CRAN (R 3.3.0)                
 data.table             1.9.6      2015-09-19 CRAN (R 3.3.0)                
 DBI                    0.5-1      2016-09-10 CRAN (R 3.3.0)                
 DESeq2                 1.12.4     2016-08-08 Bioconductor                  
 devtools               1.12.0     2016-06-24 CRAN (R 3.3.0)                
 digest                 0.6.10     2016-08-02 cran (@0.6.10)                
 doMC                   1.3.4      2015-10-13 CRAN (R 3.3.0)                
 dplyr                  0.5.0      2016-06-24 CRAN (R 3.3.0)                
 e1071                  1.6-7      2015-08-05 CRAN (R 3.3.0)                
 evaluate               0.10       2016-10-11 CRAN (R 3.3.0)                
 forcats                0.1.1      2016-09-16 CRAN (R 3.3.0)                
 foreach                1.4.3      2015-10-13 cran (@1.4.3)                 
 foreign                0.8-67     2016-09-13 CRAN (R 3.3.0)                
 formatR                1.4        2016-05-09 CRAN (R 3.3.0)                
 Formula                1.2-1      2015-04-07 CRAN (R 3.3.0)                
 genefilter             1.54.2     2016-05-16 Bioconductor                  
 geneplotter            1.50.0     2016-05-04 Bioconductor                  
 GenomeInfoDb           1.8.7      2016-09-02 Bioconductor                  
 GenomicRanges          1.24.3     2016-09-11 Bioconductor                  
 ggplot2              * 2.1.0      2016-03-01 CRAN (R 3.3.0)                
 ggrepel                0.6.3      2016-10-20 CRAN (R 3.3.0)                
 gridExtra              2.2.1      2016-02-29 CRAN (R 3.3.0)                
 gtable                 0.2.0      2016-02-26 CRAN (R 3.3.0)                
 highr                  0.6        2016-05-09 CRAN (R 3.3.0)                
 Hmisc                  3.17-4     2016-05-02 CRAN (R 3.3.0)                
 htmltools              0.3.5      2016-03-21 CRAN (R 3.3.0)                
 IRanges                2.6.1      2016-06-19 Bioconductor                  
 iterators              1.0.8      2015-10-13 cran (@1.0.8)                 
 knitr                  1.14       2016-08-13 CRAN (R 3.3.0)                
 labeling               0.3        2014-08-23 CRAN (R 3.3.0)                
 lattice              * 0.20-34    2016-09-06 CRAN (R 3.3.0)                
 latticeExtra           0.6-28     2016-02-09 CRAN (R 3.3.0)                
 lazyeval               0.2.0      2016-06-12 CRAN (R 3.3.0)                
 lme4                   1.1-12     2016-04-16 CRAN (R 3.3.0)                
 locfit                 1.5-9.1    2013-04-20 CRAN (R 3.3.0)                
 magrittr             * 1.5        2014-11-22 CRAN (R 3.3.0)                
 MASS                   7.3-45     2016-04-21 CRAN (R 3.3.0)                
 Matrix                 1.2-7.1    2016-09-01 CRAN (R 3.3.0)                
 MatrixModels           0.4-1      2015-08-22 CRAN (R 3.3.0)                
 matrixStats            0.51.0     2016-10-09 CRAN (R 3.3.0)                
 memoise                1.0.0      2016-01-29 CRAN (R 3.3.0)                
 mgcv                   1.8-15     2016-09-14 CRAN (R 3.3.0)                
 minqa                  1.2.4      2014-10-09 CRAN (R 3.3.0)                
 munsell                0.4.3      2016-02-13 CRAN (R 3.3.0)                
 nlme                   3.1-128    2016-05-10 CRAN (R 3.3.0)                
 nloptr                 1.0.4      2014-08-04 CRAN (R 3.3.0)                
 nnet                   7.3-12     2016-02-02 CRAN (R 3.3.0)                
 pbkrtest               0.4-6      2016-01-27 CRAN (R 3.3.0)                
 pheatmap               1.0.8      2015-12-11 CRAN (R 3.3.0)                
 plyr                   1.8.4      2016-06-08 CRAN (R 3.3.0)                
 purrr                  0.2.2      2016-06-18 CRAN (R 3.3.0)                
 quantreg               5.29       2016-09-04 CRAN (R 3.3.0)                
 R6                     2.2.0      2016-10-05 CRAN (R 3.3.0)                
 randomForest         * 4.6-12     2015-10-07 CRAN (R 3.3.0)                
 RColorBrewer           1.1-2      2014-12-07 CRAN (R 3.3.0)                
 Rcpp                   0.12.7     2016-09-05 cran (@0.12.7)                
 RCurl                  1.95-4.8   2016-03-01 CRAN (R 3.3.0)                
 readr                  1.0.0      2016-08-03 CRAN (R 3.3.0)                
 reshape2               1.4.2      2016-10-22 CRAN (R 3.3.0)                
 rmarkdown              1.1        2016-10-16 CRAN (R 3.3.0)                
 rpart                  4.1-10     2015-06-29 CRAN (R 3.3.0)                
 RSQLite                1.0.0      2014-10-25 CRAN (R 3.3.0)                
 S4Vectors              0.10.3     2016-08-16 Bioconductor                  
 scales                 0.4.0.9003 2016-10-24 Github (hadley/scales@d58d83a)
 SparseM                1.72       2016-09-06 CRAN (R 3.3.0)                
 stringi                1.1.2      2016-10-01 CRAN (R 3.3.0)                
 stringr                1.1.0      2016-08-19 CRAN (R 3.3.0)                
 SummarizedExperiment   1.2.3      2016-06-10 Bioconductor                  
 survival               2.39-5     2016-06-26 CRAN (R 3.3.0)                
 testthat               1.0.2      2016-04-23 CRAN (R 3.3.0)                
 tibble                 1.2        2016-08-26 cran (@1.2)                   
 tidyr                  0.6.0      2016-08-12 CRAN (R 3.3.0)                
 withr                  1.0.2      2016-06-20 CRAN (R 3.3.0)                
 XML                    3.98-1.4   2016-03-01 CRAN (R 3.3.0)                
 xtable                 1.8-2      2016-02-05 CRAN (R 3.3.0)                
 XVector                0.12.1     2016-07-22 Bioconductor                  
 yaml                   2.1.13     2014-06-12 CRAN (R 3.3.0)                
 zlibbioc               1.18.0     2016-05-04 Bioconductor