Hi,

Trying to do the following and getting an error of Model matrix not full rank:

sampleNames<-c("MMV1",    "MMV2",    "MMV3",    "FMV1",    "FMV2",    "FMV3", "MME7", "MME8", "MME9", "FME1", "FME2", "FME3")
sampleSex<-c("male", "male", "male", "female", "female", "female", "male", "male", "male", "female", "female", "female")
sampleTreatment<-c("vehicle", "vehicle", "vehicle", "vehicle", "vehicle", "vehicle", "BB", "BB", "BB", "BB", "BB", "BB")
sampleBatch<-c("1","2","3","1","2","3","4","5","6","4","5","6")
colData<-data.frame(sampleName=sampleNames, sex=sampleSex, treatment=sampleTreatment, batch=sampleBatch)

se<-SummarizedExperiment(assays=list(counts=counts),rowRanges=rowRanges, colData=colData)

table(sampleSex, sampleTreatment)

dds<-DESeqDataSet(se, design= ~ batch + sex + treatment)

converting counts to integer mode
Error in checkFullRank(modelMatrix) : 
  the model matrix is not full rank, so the model cannot be fit as specified.
  One or more variables or interaction terms in the design formula are linear
  combinations of the others and must be removed.

  Please read the vignette section 'Model matrix not full rank':



> sessionInfo()
R version 3.4.1 (2017-06-30)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS Sierra 10.12.5

Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.4/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   base     

other attached packages:
 [1] DiffBind_2.4.8                           ggplot2_2.2.1                            DESeq2_1.16.1                           
 [4] chipenrich_2.0.1                         rtracklayer_1.36.6                       TxDb.Mmusculus.UCSC.mm10.knownGene_3.4.0
 [7] org.Mm.eg.db_3.4.1                       TxDb.Mmusculus.UCSC.mm10.ensGene_3.4.0   GenomicFeatures_1.28.5                  
[10] AnnotationDbi_1.38.2                     csaw_1.10.0                              BiocParallel_1.10.1                     
[13] SummarizedExperiment_1.6.5               DelayedArray_0.2.7                       matrixStats_0.52.2                      
[16] Biobase_2.36.2                           GenomicRanges_1.28.6                     GenomeInfoDb_1.12.3                     
[19] IRanges_2.10.5                           S4Vectors_0.14.7                         BiocGenerics_0.22.1                     
[22] BiocInstaller_1.26.1                    

loaded via a namespace (and not attached):
  [1] amap_0.8-14              TH.data_1.0-8            colorspace_1.3-2         rjson_0.2.15             hwriter_1.3.2            htmlTable_1.11.1        
  [7] XVector_0.16.0           base64enc_0.1-3          rstudioapi_0.7           MatrixModels_0.4-1       ggrepel_0.7.0            bit64_0.9-7             
 [13] mvtnorm_1.0-6            org.Dr.eg.db_3.4.1       codetools_0.2-15         splines_3.4.1            chipenrich.data_2.0.0    geneplotter_1.54.0      
 [19] knitr_1.17               Formula_1.2-2            Rsamtools_1.28.0         annotate_1.54.0          cluster_2.0.6            GO.db_3.4.1             
 [25] pheatmap_1.0.8           graph_1.54.0             readr_1.1.1              compiler_3.4.1           GOstats_2.42.0           backports_1.1.2         
 [31] assertthat_0.2.0         Matrix_1.2-12            lazyeval_0.2.1           limma_3.32.10            org.Rn.eg.db_3.4.1       quantreg_5.34           
 [37] acepack_1.4.1            htmltools_0.3.6          tools_3.4.1              bindrcpp_0.2             gtable_0.2.0             glue_1.2.0              
 [43] GenomeInfoDbData_0.99.0  Category_2.42.1          systemPipeR_1.10.2       dplyr_0.7.4              ShortRead_1.34.2         Rcpp_0.12.14            
 [49] Biostrings_2.44.2        nlme_3.1-131             gdata_2.18.0             stringr_1.2.0            gtools_3.5.0             XML_3.98-1.9            
 [55] polspline_1.1.12         org.Hs.eg.db_3.4.1       edgeR_3.18.1             MASS_7.3-47              zoo_1.8-0                zlibbioc_1.22.0         
 [61] scales_0.5.0             hms_0.4.0                sandwich_2.4-0           RBGL_1.52.0              SparseM_1.77             RColorBrewer_1.1-2      
 [67] BBmisc_1.11              memoise_1.1.0            gridExtra_2.3            rms_5.1-1                biomaRt_2.32.1           rpart_4.1-11            
 [73] latticeExtra_0.6-28      stringi_1.1.6            RSQLite_2.0              Rhtslib_1.8.0            genefilter_1.58.1        checkmate_1.8.5         
 [79] caTools_1.17.1           rlang_0.1.6              pkgconfig_2.0.1          BatchJobs_1.7            bitops_1.0-6             lattice_0.20-35         
 [85] bindr_0.1                GenomicAlignments_1.12.2 htmlwidgets_0.9          bit_1.1-12               GSEABase_1.38.2          AnnotationForge_1.18.2  
 [91] plyr_1.8.4               magrittr_1.5             sendmailR_1.2-1          R6_2.2.2                 gplots_3.0.1             Hmisc_4.0-3             
 [97] multcomp_1.4-8           DBI_0.7                  mgcv_1.8-22              pillar_1.1.0             foreign_0.8-69           survival_2.41-3         
[103] RCurl_1.95-4.8           nnet_7.3-12              tibble_1.4.1             org.Dm.eg.db_3.4.1       KernSmooth_2.23-15       locfit_1.5-9.1          
[109] grid_3.4.1               data.table_1.10.4-3      blob_1.1.0               digest_0.6.14            xtable_1.8-2             brew_1.0-6              
[115] munsell_0.4.3           

  vignette('DESeq2')

You cannot use your batch information as it is nested in treatment. Try without.