Deseq2 Rlog transformation
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Entering edit mode
Sahar • 0
@7f3be7d9
Last seen 5 weeks ago
Canada

Hello,

I have data results of DESeq2, 3 samples per condition (2 conditions) When I make

boxplot(assay(rlog(dds)), outline = TRUE, col = "lightblue", xlab = "Samples", ylab = "Valeurs logarithmiques")

I get this boxplot, where all boxes are the same for all samples? Is it normal?![enter image description here][1]

> sessionInfo( )
R version 4.3.3 (2024-02-29 ucrt)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19045)

Matrix products: default


locale:
[1] LC_COLLATE=French_France.utf8  LC_CTYPE=French_France.utf8   
[3] LC_MONETARY=French_France.utf8 LC_NUMERIC=C                  
[5] LC_TIME=French_France.utf8    

time zone: America/New_York
tzcode source: internal

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

other attached packages:
 [1] ggrepel_0.9.5               EDASeq_2.36.0              
 [3] ShortRead_1.60.0            GenomicAlignments_1.38.2   
 [5] Rsamtools_2.18.0            Biostrings_2.70.3          
 [7] XVector_0.42.0              BiocParallel_1.36.0        
 [9] BiocManager_1.30.22         DESeq2_1.42.1              
[11] SummarizedExperiment_1.32.0 Biobase_2.62.0             
[13] MatrixGenerics_1.14.0       matrixStats_1.2.0          
[15] GenomicRanges_1.54.1        GenomeInfoDb_1.38.8        
[17] IRanges_2.36.0              S4Vectors_0.40.2           
[19] BiocGenerics_0.48.1         ggplot2_3.5.0              
[21] rrcov_1.7-5                 robustbase_0.99-2          

loaded via a namespace (and not attached):
  [1] RcppAnnoy_0.0.22        splines_4.3.3           later_1.3.2            
  [4] BiocIO_1.12.0           filelock_1.0.3          bitops_1.0-7           
  [7] tibble_3.2.1            R.oo_1.26.0             polyclip_1.10-6        
 [10] XML_3.99-0.16.1         fastDummies_1.7.3       lifecycle_1.0.4        
 [13] globals_0.16.3          lattice_0.22-5          MASS_7.3-60.0.1        
 [16] magrittr_2.0.3          plotly_4.10.4           yaml_2.3.8             
 [19] httpuv_1.6.15           Seurat_5.0.3            sctransform_0.4.1      
 [22] spam_2.10-0             sp_2.1-3                spatstat.sparse_3.0-3  
 [25] EnhancedVolcano_1.20.0  reticulate_1.35.0       DBI_1.2.2              
 [28] cowplot_1.1.3           pbapply_1.7-2           RColorBrewer_1.1-3     
 [31] abind_1.4-5             pkgload_1.3.4           zlibbioc_1.48.0        
 [34] Rtsne_0.17              purrr_1.0.2             R.utils_2.12.3         
 [37] RCurl_1.98-1.14         rappdirs_0.3.3          GenomeInfoDbData_1.2.11
 [40] irlba_2.3.5.1           listenv_0.9.1           spatstat.utils_3.0-4   
 [43] goftest_1.2-3           RSpectra_0.16-1         spatstat.random_3.2-3  
 [46] fitdistrplus_1.1-11     parallelly_1.37.1       leiden_0.4.3.1         
 [49] codetools_0.2-19        DelayedArray_0.28.0     xml2_1.3.6             
 [52] tidyselect_1.2.1        farver_2.1.1            BiocFileCache_2.10.2   
 [55] spatstat.explore_3.2-7  jsonlite_1.8.8          progressr_0.14.0       
 [58] ggridges_0.5.6          survival_3.5-8          progress_1.2.3         
 [61] tools_4.3.3             ica_1.0-3               Rcpp_1.0.12            
 [64] glue_1.7.0              gridExtra_2.3           SparseArray_1.2.4      
 [67] dplyr_1.1.4             withr_3.0.0             fastmap_1.1.1          
 [70] latticeExtra_0.6-30     fansi_1.0.6             digest_0.6.35          
 [73] R6_2.5.1                mime_0.12               colorspace_2.1-0       
 [76] scattermore_1.2         tensor_1.5              RSQLite_2.3.6          
 [79] jpeg_0.1-10             spatstat.data_3.0-4     biomaRt_2.58.2         
 [82] R.methodsS3_1.8.2       utf8_1.2.4              tidyr_1.3.1            
 [85] generics_0.1.3          data.table_1.15.4       rtracklayer_1.62.0     
 [88] prettyunits_1.2.0       httr_1.4.7              htmlwidgets_1.6.4      
 [91] S4Arrays_1.2.1          uwot_0.1.16             pkgconfig_2.0.3        
 [94] gtable_0.3.4            blob_1.2.4              lmtest_0.9-40          
 [97] hwriter_1.3.2.1         pcaPP_2.0-4             htmltools_0.5.8.1      
[100] dotCall64_1.1-1         SeuratObject_5.0.1      scales_1.3.0           
[103] png_0.1-8               rstudioapi_0.16.0       rjson_0.2.21           
[106] reshape2_1.4.4          curl_5.2.1              nlme_3.1-164           
[109] cachem_1.0.8            zoo_1.8-12              stringr_1.5.1          
[112] KernSmooth_2.23-22      parallel_4.3.3          miniUI_0.1.1.1         
[115] AnnotationDbi_1.64.1    restfulr_0.0.15         pillar_1.9.0           
[118] grid_4.3.3              vctrs_0.6.5             RANN_2.6.1             
[121] promises_1.3.0          dbplyr_2.5.0            xtable_1.8-4           
[124] cluster_2.1.6           GenomicFeatures_1.54.4  mvtnorm_1.2-4          
[127] cli_3.6.1               locfit_1.5-9.9          compiler_4.3.3         
[130] rlang_1.1.1             crayon_1.5.2            future.apply_1.11.2    
[133] labeling_0.4.3          interp_1.1-6            aroma.light_3.32.0     
[136] plyr_1.8.9              stringi_1.8.3           viridisLite_0.4.2      
[139] deldir_2.0-4            munsell_0.5.1           lazyeval_0.2.2         
[142] spatstat.geom_3.2-9     Matrix_1.6-5            RcppHNSW_0.6.0         
[145] hms_1.1.3               patchwork_1.2.0         bit64_4.0.5            
[148] future_1.33.2           KEGGREST_1.42.0         shiny_1.8.1.1          
[151] ROCR_1.0-11             memoise_2.0.1           igraph_2.0.3           
[154] bit_4.0.5               DEoptimR_1.1-3
DESeq2 • 156 views
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