Hello,
I have two versions of DESeq2, 1.14 and 1.16. I run the following code:
dds <- makeExampleDESeqDataSet(n=100,m=12) dds$genotype <- factor(rep(rep(c("I","II"),each=3),2)) design(dds) <- ~ genotype + condition dds <- DESeq(dds) resultsNames(dds)
For the version 1.14 it produces the following output:
[1] "Intercept" "genotypeI" "genotypeII" "conditionA" "conditionB"
And for the version 1.16 the following:
[1] "Intercept" "genotype_II_vs_I" "condition_B_vs_A"
My question is, if on the version 1.16 it is possible to revert to the 1.14 output (single levels of factors) in order to make analysis like DESeq2 likelihood ratio test (LRT) design - 2 genotypes, 4 time points?
Session info of the 1.14:
R version 3.3.1 (2016-06-21) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Ubuntu 14.04.5 LTS locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=de_DE.UTF-8 LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=de_DE.UTF-8 LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=de_DE.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=de_DE.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] parallel stats4 stats graphics grDevices utils datasets [8] methods base other attached packages: [1] DESeq2_1.14.1 SummarizedExperiment_1.4.0 [3] Biobase_2.34.0 GenomicRanges_1.26.4 [5] GenomeInfoDb_1.10.3 IRanges_2.8.2 [7] S4Vectors_0.12.2 BiocGenerics_0.20.0 loaded via a namespace (and not attached): [1] genefilter_1.56.0 locfit_1.5-9.1 splines_3.3.1 [4] lattice_0.20-35 colorspace_1.3-2 htmltools_0.3.6 [7] base64enc_0.1-3 blob_1.1.0 survival_2.41-3 [10] XML_3.98-1.9 rlang_0.1.1 foreign_0.8-69 [13] DBI_0.7 BiocParallel_1.8.2 bit64_0.9-7 [16] RColorBrewer_1.1-2 plyr_1.8.4 stringr_1.2.0 [19] zlibbioc_1.20.0 munsell_0.4.3 gtable_0.2.0 [22] htmlwidgets_0.8 memoise_1.1.0 latticeExtra_0.6-28 [25] knitr_1.16 geneplotter_1.52.0 AnnotationDbi_1.36.2 [28] htmlTable_1.9 Rcpp_0.12.11 acepack_1.4.1 [31] xtable_1.8-2 scales_0.4.1 backports_1.1.0 [34] checkmate_1.8.3 Hmisc_4.0-3 annotate_1.52.1 [37] XVector_0.14.1 bit_1.1-12 gridExtra_2.2.1 [40] ggplot2_2.2.1 digest_0.6.12 stringi_1.1.5 [43] grid_3.3.1 bitops_1.0-6 tools_3.3.1 [46] magrittr_1.5 lazyeval_0.2.0 RCurl_1.95-4.8 [49] tibble_1.3.3 RSQLite_2.0 Formula_1.2-1 [52] cluster_2.0.6 Matrix_1.2-10 data.table_1.10.4 [55] rpart_4.1-11 nnet_7.3-12
Session info of the 1.16:
R version 3.4.0 (2017-04-21) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Red Hat Enterprise Linux Matrix products: default BLAS: /usr/local/lib64/R/lib/libRblas.so LAPACK: /usr/local/lib64/R/lib/libRlapack.so locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=de_DE.UTF-8 LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=de_DE.UTF-8 LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=de_DE.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=de_DE.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] parallel stats4 stats graphics grDevices utils datasets [8] methods base other attached packages: [1] DESeq2_1.16.1 SummarizedExperiment_1.6.1 [3] DelayedArray_0.2.2 matrixStats_0.52.2 [5] Biobase_2.36.2 GenomicRanges_1.28.2 [7] GenomeInfoDb_1.12.0 IRanges_2.10.1 [9] S4Vectors_0.14.1 BiocGenerics_0.22.0 loaded via a namespace (and not attached): [1] genefilter_1.58.1 locfit_1.5-9.1 splines_3.4.0 [4] lattice_0.20-35 colorspace_1.3-2 htmltools_0.3.6 [7] base64enc_0.1-3 survival_2.41-3 XML_3.98-1.7 [10] rlang_0.1.1 DBI_0.6-1 foreign_0.8-68 [13] BiocParallel_1.10.1 RColorBrewer_1.1-2 GenomeInfoDbData_0.99.0 [16] plyr_1.8.4 stringr_1.2.0 zlibbioc_1.22.0 [19] munsell_0.4.3 gtable_0.2.0 htmlwidgets_0.8 [22] memoise_1.1.0 latticeExtra_0.6-28 knitr_1.15.1 [25] geneplotter_1.54.0 AnnotationDbi_1.38.0 htmlTable_1.9 [28] Rcpp_0.12.10 acepack_1.4.1 xtable_1.8-2 [31] scales_0.4.1 backports_1.0.5 checkmate_1.8.2 [34] Hmisc_4.0-3 annotate_1.54.0 XVector_0.16.0 [37] gridExtra_2.2.1 ggplot2_2.2.1 digest_0.6.12 [40] stringi_1.1.5 grid_3.4.0 tools_3.4.0 [43] bitops_1.0-6 magrittr_1.5 RSQLite_1.1-2 [46] lazyeval_0.2.0 RCurl_1.95-4.8 tibble_1.3.1 [49] Formula_1.2-1 cluster_2.0.6 Matrix_1.2-10 [52] data.table_1.10.4 rpart_4.1-11 nnet_7.3-12 [55] compiler_3.4.0