DEseq2 complex design - 2 factors with more than 2 levels
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Bio • 0
@bio-23985
Last seen 2 days ago

Hi all!

Using DEseq2 (v 1.30.0) I try to analyze a "complex" data set with 2 factors (A and B) harboring different levels. Factor A (named hereafter "line") has two levels (infected/non-infected) and factor 2 (named hereafter "group") has 4 (non-infected, mono-infected with 1, mono-infected with 2 and bi-infected with 1 and 2 at the same time). According to phenotype data, what drives my phenotype is A:B interaction. Thereby, I try to find the genes that are explained by interaction A:B. I guess that the trick is to use contrasts methods, but I am positively lost between all the lists of genes to find the one I am interested in (if there is only one), in addition to the fact that DEseq2 asks for a "reference" level which does not make really sense in an interaction model. Do you have any clues to help me? When I use the #resultsNames function, where should I look? What would be the correct coding for contrasts?

Thanks a lot for your help. -Vincent

Code should be placed in three backticks as shown below


cts <- read.delim("Pupalcountstotal.txt", header=TRUE, row.names="GeneID")
coldata <- read.delim("design.txt", header=TRUE) #24 obs

coldata$group <- as.factor(coldata$group)
coldata$line <- as.factor(coldata$line)


dds <- DESeqDataSetFromMatrix(countData = cts,
                              colData = coldata,
                              design= ~ group+line+group:line)

#remove <100 counts total per transcript
dds <- dds[ rowSums(counts(dds)) > 100, ] #reste 13169

#relevel factors
dds$group <- relevel(dds$group, ref = "GF")
dds$line <- relevel(dds$line, ref = "wolb")


dds <- DESeq(dds)
resultsNames(dds) 

[1] "Intercept"        "group_AP_vs_GF"   "group_BI_vs_GF"   "group_LP_vs_GF"   "line_tet_vs_wolb" "groupAP.linetet"  "groupBI.linetet" 
[8] "groupLP.linetet" 

sessionInfo( )
R version 4.0.3 (2020-10-10)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Catalina 10.15.7

Matrix products: default
BLAS:   /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRlapack.dylib

Random number generation:
 RNG:     Mersenne-Twister 
 Normal:  Inversion 
 Sample:  Rounding 

locale:
[1] fr_FR.UTF-8/fr_FR.UTF-8/fr_FR.UTF-8/C/fr_FR.UTF-8/fr_FR.UTF-8

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

other attached packages:
 [1] SARTools_1.7.3              kableExtra_1.3.1            emmeans_1.5.3               devtools_2.3.2              usethis_2.0.0              
 [6] edgeR_3.32.0                limma_3.46.0                DESeq2_1.30.0               SummarizedExperiment_1.20.0 Biobase_2.50.0             
[11] MatrixGenerics_1.2.0        matrixStats_0.57.0          GenomicRanges_1.42.0        GenomeInfoDb_1.26.2         IRanges_2.24.1             
[16] S4Vectors_0.28.1            BiocGenerics_0.36.0         gprofiler2_0.2.0            UpSetR_1.4.0                coxme_2.2-16               
[21] bdsmatrix_1.3-4             scales_1.1.1                viridis_0.5.1               viridisLite_0.3.0           car_3.0-10                 
[26] carData_3.0-4               GGally_2.1.0                survival_3.2-7              lme4_1.1-26                 Matrix_1.2-18              
[31] gplots_3.1.1                knitr_1.30                  reshape2_1.4.4              gridExtra_2.3               stringr_1.4.0              
[36] plyr_1.8.6                  ggplot2_3.3.3               MASS_7.3-53                

loaded via a namespace (and not attached):
  [1] readxl_1.3.1           lazyeval_0.2.2         splines_4.0.3          BiocParallel_1.24.1    TH.data_1.0-10         digest_0.6.27         
  [7] htmltools_0.5.0        fansi_0.4.1            magrittr_2.0.1         memoise_1.1.0          openxlsx_4.2.3         remotes_2.2.0         
 [13] annotate_1.68.0        sandwich_3.0-0         prettyunits_1.1.1      colorspace_2.0-0       ggrepel_0.9.0          rvest_0.3.6           
 [19] blob_1.2.1             haven_2.3.1            xfun_0.20              dplyr_1.0.2            callr_3.5.1            crayon_1.3.4          
 [25] RCurl_1.98-1.2         jsonlite_1.7.2         genefilter_1.72.0      zoo_1.8-8              glue_1.4.2             gtable_0.3.0          
 [31] zlibbioc_1.36.0        XVector_0.30.0         webshot_0.5.2          DelayedArray_0.16.0    pkgbuild_1.2.0         abind_1.4-5           
 [37] mvtnorm_1.1-1          DBI_1.1.0              Rcpp_1.0.5             xtable_1.8-4           foreign_0.8-81         bit_4.0.4             
 [43] htmlwidgets_1.5.3      httr_1.4.2             RColorBrewer_1.1-2     ellipsis_0.3.1         farver_2.0.3           pkgconfig_2.0.3       
 [49] reshape_0.8.8          XML_3.99-0.5           locfit_1.5-9.4         labeling_0.4.2         tidyselect_1.1.0       rlang_0.4.10          
 [55] AnnotationDbi_1.52.0   munsell_0.5.0          cellranger_1.1.0       tools_4.0.3            cli_2.2.0              generics_0.1.0        
 [61] RSQLite_2.2.1          ggdendro_0.1.22        evaluate_0.14          processx_3.4.5         bit64_4.0.5            fs_1.5.0              
 [67] zip_2.1.1              caTools_1.18.0         purrr_0.3.4            nlme_3.1-151           xml2_1.3.2             compiler_4.0.3        
 [73] rstudioapi_0.13        plotly_4.9.2.2         curl_4.3               testthat_3.0.1         tibble_3.0.4           statmod_1.4.35        
 [79] geneplotter_1.68.0     stringi_1.5.3          ps_1.5.0               desc_1.2.0             forcats_0.5.0          lattice_0.20-41       
 [85] nloptr_1.2.2.2         vctrs_0.3.6            pillar_1.4.7           lifecycle_0.2.0        estimability_1.3       data.table_1.13.6     
 [91] bitops_1.0-6           R6_2.5.0               KernSmooth_2.23-18     rio_0.5.16             sessioninfo_1.1.1      codetools_0.2-18      
 [97] boot_1.3-25            gtools_3.8.2           assertthat_0.2.1       pkgload_1.1.0          rprojroot_2.0.2        withr_2.3.0           
[103] multcomp_1.4-15        GenomeInfoDbData_1.2.4 hms_0.5.3              tidyr_1.1.2            coda_0.19-4            minqa_1.2.4           
[109] rmarkdown_2.6          tinytex_0.28
DESeq2 • 48 views
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@mikelove
Last seen 2 days ago
United States

For questions about how to set up the statistical design for your problem, I recommend to work with a local statistician.

Unfortunately, I'm limited in the time I can spend on the support site, and have to restrict myself to software-related questions.

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