Hi all, I would like to use DESeq2 to analyze bulk RNA-seq data and I have the following coldata:
group donor id
wt_ctrl m1 wt_ctrl_m1
wt_treated m1 wt_treated_m1
wt_ctrl m2 wt_ctrl_m2
wt_treated m2 wt_treated_m2
ko_treated m3 ko_treated_m3
ko_ctrl m3 ko_ctrl_m3
ko_ctrl m4 ko_ctrl_m4
ko_treated m4 ko_treated_m4
ko_ctrl m5 ko_ctrl_m5
wt_treated m6 wt_treated_m6
wt_ctrl m6 wt_ctrl_m6
ko_treated m5 ko_treated_m5
ko_ctrl m7 ko_ctrl_m7
ko_treated m7 ko_treated_m7
wt_treated m8 wt_treated_m8
wt_cntrl m8 wt_cntrl_m8
wt_treated m9 wt_treated_m9
wt_ctrl m9 wt_ctrl_m9
ko_treated m10 ko_treated_m10
ko_ctrl m10 ko_ctrl_m10
I wanted to perform DE analysis, so to create the dds object
dds <- DESeqDataSet(gse1, design = ~donor + group)
but I got the following error
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':
vignette('DESeq2')
So I tried to find from the vignette a work around to include both donor and group in my design:
dds <- DESeqDataSet(gse, design = ~ donor + donor:id+ donor:group)
then when I wanted to run DESeq()
I got the follwoing error:
Error in designAndArgChecker(object, betaPrior) :
full model matrix is less than full rank
I am a bit confused how to handle this design:
table(gse1$donor_animal,gse1$group)
wt_ctrl wt_treated ko_ctrl ko_treated
m1 1 1 0 0
m10 0 0 1 1
m2 1 1 0 0
m3 0 0 1 1
m4 0 0 1 1
m5 0 0 1 1
m6 1 1 0 0
m7 0 0 1 1
m8 1 1 0 0
m9 1 1 0 0
even when we see that the wt and ko columns are duplicated. Any ideas on how should I proceed? Thank you in advance!
sessionInfo( )
R version 4.4.1 (2024-06-14)
Platform: aarch64-apple-darwin20
Running under: macOS Ventura 13.6
Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libRlapack.dylib; LAPACK version 3.12.0
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
time zone: Europe/Berlin
tzcode source: internal
attached base packages:
[1] stats4 stats graphics grDevices utils datasets methods base
other attached packages:
[1] tximeta_1.23.2 topGO_2.57.0
[3] SparseM_1.84-2 GO.db_3.19.1
[5] graph_1.83.0 clusterProfiler_4.13.3
[7] biomaRt_2.61.3 org.Mm.eg.db_3.19.1
[9] AnnotationDbi_1.67.0 DT_0.33
[11] GeneTonic_2.9.0 DESeq2_1.45.3
[13] pcaExplorer_2.31.0 limma_3.61.9
[15] ggplot2_3.5.1 knitr_1.48
[17] SingleCellExperiment_1.27.2 SummarizedExperiment_1.35.1
[19] Biobase_2.65.1 GenomicRanges_1.57.1
[21] GenomeInfoDb_1.41.1 IRanges_2.39.2
[23] S4Vectors_0.43.2 BiocGenerics_0.51.1
[25] MatrixGenerics_1.17.0 matrixStats_1.4.1
loaded via a namespace (and not attached):
[1] ProtGenerics_1.37.1 fs_1.6.4 bitops_1.0-8
[4] enrichplot_1.25.2 httr_1.4.7 webshot_0.5.5
[7] RColorBrewer_1.1-3 doParallel_1.0.17 Rgraphviz_2.49.0
[10] dynamicTreeCut_1.63-1 tippy_0.1.0 tools_4.4.1
[13] utf8_1.2.4 R6_2.5.1 lazyeval_0.2.2
[16] GetoptLong_1.0.5 withr_3.0.1 prettyunits_1.2.0
[19] gridExtra_2.3 cli_3.6.3 TSP_1.2-4
[22] scatterpie_0.2.4 labeling_0.4.3 sass_0.4.9
[25] bs4Dash_2.3.4 genefilter_1.87.0 ggridges_0.5.6
[28] Rsamtools_2.21.1 yulab.utils_0.1.7 txdbmaker_1.1.1
[31] gson_0.1.0 DOSE_3.99.1 R.utils_2.12.3
[34] AnnotationForge_1.47.1 readxl_1.4.3 rstudioapi_0.16.0
[37] RSQLite_2.3.7 BiocIO_1.15.2 gridGraphics_0.5-1
[40] visNetwork_2.1.2 generics_0.1.3 GOstats_2.71.0
[43] shape_1.4.6.1 crosstalk_1.2.1 dplyr_1.1.4
[46] dendextend_1.17.1 Matrix_1.7-0 fansi_1.0.6
[49] abind_1.4-8 R.methodsS3_1.8.2 lifecycle_1.0.4
[52] yaml_2.3.10 qvalue_2.37.0 SparseArray_1.5.36
[55] BiocFileCache_2.13.0 grid_4.4.1 blob_1.2.4
[58] promises_1.3.0 crayon_1.5.3 shinydashboard_0.7.2
[61] miniUI_0.1.1.1 lattice_0.22-6 cowplot_1.1.3
[64] ComplexUpset_1.3.3 GenomicFeatures_1.57.0 annotate_1.83.0
[67] KEGGREST_1.45.1 pillar_1.9.0 ComplexHeatmap_2.21.0
[70] fgsea_1.31.0 rjson_0.2.23 codetools_0.2-20
[73] fastmatch_1.1-4 glue_1.7.0 ggfun_0.1.6
[76] data.table_1.16.0 treeio_1.29.1 vctrs_0.6.5
[79] png_0.1-8 cellranger_1.1.0 gtable_0.3.5
[82] assertthat_0.2.1 cachem_1.1.0 xfun_0.47
[85] S4Arrays_1.5.7 mime_0.12 tidygraph_1.3.1
[88] survival_3.7-0 pheatmap_1.0.12 seriation_1.5.6
[91] iterators_1.0.14 statmod_1.5.0 nlme_3.1-166
[94] Category_2.71.0 ggtree_3.13.1 bit64_4.5.2
[97] threejs_0.3.3 progress_1.2.3 filelock_1.0.3
[100] bslib_0.8.0 colorspace_2.1-1 DBI_1.2.3
[103] tidyselect_1.2.1 bit_4.5.0 compiler_4.4.1
[106] curl_5.2.3 httr2_1.0.4 expm_1.0-0
[109] xml2_1.3.6 DelayedArray_0.31.11 plotly_4.10.4
[112] rtracklayer_1.65.0 shadowtext_0.1.4 colourpicker_1.3.0
[115] scales_1.3.0 RBGL_1.81.0 NMF_0.28
[118] rappdirs_0.3.3 stringr_1.5.1 digest_0.6.37
[121] shinyBS_0.61.1 rmarkdown_2.28 ca_0.71.1
[124] XVector_0.45.0 htmltools_0.5.8.1 pkgconfig_2.0.3
[127] base64enc_0.1-3 ensembldb_2.29.1 dbplyr_2.5.0
[130] fastmap_1.2.0 rlang_1.1.4 GlobalOptions_0.1.2
[133] htmlwidgets_1.6.4 UCSC.utils_1.1.0 shiny_1.9.1
[136] farver_2.1.2 jquerylib_0.1.4 jsonlite_1.8.9
[139] BiocParallel_1.39.0 GOSemSim_2.31.2 R.oo_1.26.0
[142] RCurl_1.98-1.16 magrittr_2.0.3 ggplotify_0.1.2
[145] GenomeInfoDbData_1.2.12 patchwork_1.3.0 munsell_0.5.1
[148] Rcpp_1.0.13 ape_5.8 shinycssloaders_1.1.0
[151] viridis_0.6.5 stringi_1.8.4 rintrojs_0.3.4
[154] ggraph_2.2.1 zlibbioc_1.51.1 MASS_7.3-61
[157] AnnotationHub_3.13.3 plyr_1.8.9 parallel_4.4.1
[160] ggrepel_0.9.6 graphlayouts_1.2.0 Biostrings_2.73.1
[163] splines_4.4.1 hms_1.1.3 circlize_0.4.16
[166] locfit_1.5-9.10 igraph_2.0.3 rngtools_1.5.2
[169] pkgload_1.4.0 reshape2_1.4.4 BiocVersion_3.20.0
[172] XML_3.99-0.17 evaluate_1.0.0 BiocManager_1.30.25
[175] foreach_1.5.2 tweenr_2.0.3 httpuv_1.6.15
[178] backbone_2.1.4 tidyr_1.3.1 purrr_1.0.2
[181] polyclip_1.10-7 heatmaply_1.5.0 clue_0.3-65
[184] gridBase_0.4-7 ggforce_0.4.2 xtable_1.8-4
[187] AnnotationFilter_1.29.0 restfulr_0.0.15 tidytree_0.4.6
[190] later_1.3.2 viridisLite_0.4.2 tibble_3.2.1
[193] aplot_0.2.3 GenomicAlignments_1.41.0 memoise_2.0.1
[196] registry_0.5-1 tximport_1.33.0 cluster_2.1.6
[199] shinyWidgets_0.8.7 shinyAce_0.4.2 GSEABase_1.67.0