Using group instead of interaction term on a custom edited matrix
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Entering edit mode
jd348 • 0
@user-24862
Last seen 13 days ago
Durham

Hello,

After reading the vignette, I decided to combine factors of interest into a single group (in this case it is Age and Genotype) rather than using an interaction term. I am interested in comparing differences between genotypes at certain ages of animals. I manually edited my matrix because there are levels without samples. When I attempt to pass in my manually edited matrix with the combined factors, I receive the error Error in solve.default(qr.R(qrx)) : 'a' (1 x 0) must be square

Here is what my data looks like:data set


ddsHTSeq <- DESeqDataSetFromHTSeqCount(sampleTable = sampletable_med,
                                       directory = directory,
                                       design = ~ 1)
# filter low counts
  # keep only those genes that have more than 10 summed raw counts across the samples
ddsHTSeq_filtered <- ddsHTSeq[rowSums(counts(ddsHTSeq)) > 10, ]

# manually edit matrix to remove levels without samples
ddsHTSeq_filtered$group <- factor(paste0(ddsHTSeq_filtered$Genotype, ddsHTSeq_filtered$Age))
custom.matrix <- model.matrix(~ group, data = colData(ddsHTSeq_filtered))
all.zero <- apply(custom.matrix, 2, function(x) all(x==0))
idx <- which(all.zero)
custom.matrix <- custom.matrix[,-idx]

# fit statistical model
dds <- DESeq(ddsHTSeq_filtered, full = custom.matrix)

sessionInfo( )
R version 3.6.2 (2019-12-12)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS Mojave 10.14

Matrix products: default
BLAS:   /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.6/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] org.Mm.eg.db_3.10.0         GOstats_2.52.0              graph_1.64.0                Category_2.52.1             Matrix_1.3-2               
 [6] GO.db_3.10.0                AnnotationDbi_1.48.0        genefilter_1.68.0           RColorBrewer_1.1-2          gplots_3.1.1               
[11] forcats_0.5.1               stringr_1.4.0               dplyr_1.0.4                 purrr_0.3.4                 readr_1.4.0                
[16] tidyr_1.1.2                 tibble_3.0.6                tidyverse_1.3.0             ggplot2_3.3.3               pheatmap_1.0.12            
[21] apeglm_1.8.0                DESeq2_1.26.0               SummarizedExperiment_1.16.1 DelayedArray_0.12.3         BiocParallel_1.20.1        
[26] matrixStats_0.58.0          Biobase_2.46.0              GenomicRanges_1.38.0        GenomeInfoDb_1.22.1         IRanges_2.20.2             
[31] S4Vectors_0.24.4            BiocGenerics_0.32.0        

loaded via a namespace (and not attached):
 [1] colorspace_2.0-0       ellipsis_0.3.1         htmlTable_2.1.0        XVector_0.26.0         base64enc_0.1-3        fs_1.5.0              
 [7] rstudioapi_0.13        farver_2.0.3           bit64_4.0.5            fansi_0.4.2            mvtnorm_1.1-1          lubridate_1.7.9.2     
[13] xml2_1.3.2             splines_3.6.2          cachem_1.0.4           geneplotter_1.64.0     knitr_1.31             Formula_1.2-4         
[19] jsonlite_1.7.2         broom_0.7.5            annotate_1.64.0        cluster_2.1.1          dbplyr_2.1.0           png_0.1-7             
[25] compiler_3.6.2         httr_1.4.2             backports_1.2.1        assertthat_0.2.1       fastmap_1.1.0          cli_2.3.1             
[31] htmltools_0.5.1.1      tools_3.6.2            coda_0.19-4            gtable_0.3.0           glue_1.4.2             GenomeInfoDbData_1.2.2
[37] Rcpp_1.0.6             bbmle_1.0.23.1         cellranger_1.1.0       vctrs_0.3.6            xfun_0.21              rvest_0.3.6           
[43] lifecycle_1.0.0        gtools_3.8.2           XML_3.99-0.3           zlibbioc_1.32.0        MASS_7.3-53.1          scales_1.1.1          
[49] hms_1.0.0              RBGL_1.62.1            memoise_2.0.0          gridExtra_2.3          emdbook_1.3.12         bdsmatrix_1.3-4       
[55] rpart_4.1-15           latticeExtra_0.6-29    stringi_1.5.3          RSQLite_2.2.3          checkmate_2.0.0        caTools_1.18.1        
[61] rlang_0.4.10           pkgconfig_2.0.3        bitops_1.0-6           lattice_0.20-41        labeling_0.4.2         htmlwidgets_1.5.3     
[67] bit_4.0.4              tidyselect_1.1.0       AnnotationForge_1.28.0 GSEABase_1.48.0        plyr_1.8.6             magrittr_2.0.1        
[73] R6_2.5.0               generics_0.1.0         Hmisc_4.4-2            DBI_1.1.1              pillar_1.5.0           haven_2.3.1           
[79] foreign_0.8-75         withr_2.4.1            survival_3.2-7         RCurl_1.98-1.2         nnet_7.3-15            modelr_0.1.8          
[85] crayon_1.4.1           KernSmooth_2.23-18     utf8_1.1.4             jpeg_0.1-8.1           locfit_1.5-9.4         grid_3.6.2            
[91] readxl_1.3.1           data.table_1.13.6      Rgraphviz_2.30.0       blob_1.2.1             reprex_1.0.0           digest_0.6.27         
[97] xtable_1.8-4           numDeriv_2016.8-1.1    munsell_0.5.0
DESeq2 • 77 views
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3
Entering edit mode
@mikelove
Last seen 18 hours ago
United States

You don't need to provide a custom matrix, just follow the guidelines in the vignette using factor(paste0()).

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