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 3.3.1 (2016-06-21)
 system   x86_64, darwin13.4.0        
 ui       X11                         
 language (EN)                        
 collate  en_CA.UTF-8                 
 tz       America/Vancouver           
 date     2016-12-03                  

 package              * version  date       source        
 acepack                1.4.1    2016-10-29 CRAN (R 3.3.0)
 annotate               1.52.0   2016-10-18 Bioconductor  
 AnnotationDbi          1.36.0   2016-10-18 Bioconductor  
 assertthat             0.1      2013-12-06 CRAN (R 3.3.0)
 backports              1.0.4    2016-10-24 CRAN (R 3.3.0)
 Biobase                2.34.0   2016-10-18 Bioconductor  
 BiocGenerics           0.20.0   2016-10-18 Bioconductor  
 BiocParallel           1.8.1    2016-10-30 Bioconductor  
 biomaRt                2.30.0   2016-10-18 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                * 6.0-73   2016-11-10 CRAN (R 3.3.2)
 class                  7.3-14   2015-08-30 CRAN (R 3.3.1)
 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             1.3-1    2016-11-18 CRAN (R 3.3.2)
 cowplot                0.7.0    2016-10-28 CRAN (R 3.3.0)
 crayon                 1.3.2    2016-06-28 CRAN (R 3.3.0)
 data.table             1.9.8    2016-11-25 CRAN (R 3.3.2)
 DBI                    0.5-1    2016-09-10 CRAN (R 3.3.0)
 DESeq2                 1.14.0   2016-10-18 Bioconductor  
 devtools               1.12.0   2016-06-24 CRAN (R 3.3.0)
 digest                 0.6.10   2016-08-02 CRAN (R 3.3.0)
 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 (R 3.3.0)
 foreign                0.8-67   2016-09-13 CRAN (R 3.3.0)
 Formula                1.2-1    2015-04-07 CRAN (R 3.3.0)
 genefilter             1.56.0   2016-10-18 Bioconductor  
 geneplotter            1.52.0   2016-10-18 Bioconductor  
 GenomeInfoDb           1.10.1   2016-11-04 Bioconductor  
 GenomicRanges          1.26.1   2016-10-20 Bioconductor  
 ggplot2              * 2.2.0    2016-11-11 CRAN (R 3.3.2)
 ggrepel                0.6.5    2016-11-24 CRAN (R 3.3.2)
 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                  4.0-0    2016-11-01 CRAN (R 3.3.0)
 htmlTable              1.7      2016-10-19 CRAN (R 3.3.0)
 htmltools              0.3.5    2016-03-21 CRAN (R 3.3.0)
 IRanges                2.8.1    2016-11-08 Bioconductor  
 iterators              1.0.8    2015-10-13 CRAN (R 3.3.0)
 knitr                  1.15.1   2016-11-22 CRAN (R 3.3.2)
 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 3.3.1)
 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                   1.8-16   2016-11-07 CRAN (R 3.3.0)
 minqa                  1.2.4    2014-10-09 CRAN (R 3.3.0)
 ModelMetrics           1.1.0    2016-08-26 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 3.3.1)
 nloptr                 1.0.4    2014-08-04 CRAN (R 3.3.0)
 nnet                   7.3-12   2016-02-02 CRAN (R 3.3.1)
 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                   0.12.8   2016-11-17 CRAN (R 3.3.2)
 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              1.2      2016-11-21 CRAN (R 3.3.2)
 rpart                  4.1-10   2015-06-29 CRAN (R 3.3.1)
 rprojroot              1.1      2016-10-29 CRAN (R 3.3.0)
 RSQLite                1.1      2016-11-27 CRAN (R 3.3.0)
 rstudioapi             0.6      2016-06-27 CRAN (R 3.3.0)
 S4Vectors              0.12.0   2016-10-18 Bioconductor  
 scales                 0.4.1    2016-11-09 CRAN (R 3.3.2)
 SparseM                1.74     2016-11-10 CRAN (R 3.3.2)
 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   1.4.0    2016-10-18 Bioconductor  
 survival               2.40-1   2016-10-30 CRAN (R 3.3.0)
 testthat               1.0.2    2016-04-23 CRAN (R 3.3.0)
 tibble                 1.2      2016-08-26 CRAN (R 3.3.0)
 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                    3.98-1.5 2016-11-10 CRAN (R 3.3.2)
 xtable                 1.8-2    2016-02-05 CRAN (R 3.3.0)
 XVector                0.14.0   2016-10-18 Bioconductor  
 yaml                   2.1.14   2016-11-12 CRAN (R 3.3.2)
 zlibbioc               1.20.0   2016-10-18 Bioconductor