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Author: wolski

articles/Comparing2Groups.html

@@ -519,7 +519,7 @@ sessionInfo()
     ## 
     ## loaded via a namespace (and not attached):
     ##  [1] gtable_0.3.6        xfun_0.56           bslib_0.10.0       
-    ##  [4] ggplot2_4.0.2       htmlwidgets_1.6.4   ggrepel_0.9.7      
+    ##  [4] ggplot2_4.0.2       htmlwidgets_1.6.4   ggrepel_0.9.8      
     ##  [7] vctrs_0.7.1         tools_4.5.2         crosstalk_1.2.2    
     ## [10] generics_0.1.4      tibble_3.3.1        pkgconfig_2.0.3    
     ## [13] pheatmap_1.0.13     KernSmooth_2.23-26  data.table_1.18.2.1

articles/Comparing2Groups.md

@@ -217,6 +217,44 @@ results_protein |>
     ## 10 firth  WaldTestFirth  OrL0ux~1369 -1.69  2.51e- 1 1            
     ## # ℹ 15 more rows
 
+## Proteins dropped by lm but retained by limma
+
+The `lm` facade filters proteins more strictly than limma — it requires
+all model coefficients to be estimable and at least 2 residual degrees
+of freedom. Limma handles partial missingness internally per row. Here
+we identify the proteins that limma reports but `lm` does not, and show
+their per-sample intensities.
+
+``` r
+proteins_lm <- fa_lm$get_contrasts() |> dplyr::pull(protein_Id) |> unique()
+proteins_limma <- fa_limma$get_contrasts() |> dplyr::pull(protein_Id) |> unique()
+dropped <- setdiff(proteins_limma, proteins_lm)
+message("Proteins in limma but not in lm: ", length(dropped))
+```
+
+``` r
+if (length(dropped) > 0) {
+  lfq_protein$data |>
+    dplyr::filter(protein_Id %in% dropped) |>
+    dplyr::select(protein_Id, sampleName,
+                  !!rlang::sym(lfq_protein$config$get_response())) |>
+    tidyr::pivot_wider(names_from = sampleName,
+                       values_from = !!rlang::sym(lfq_protein$config$get_response())) |>
+    knitr::kable(digits = 2, caption = "Per-sample intensities of proteins dropped by lm")
+}
+```
+
+| protein_Id  | B_V1 | B_V4 | Ctrl_V3 | Ctrl_V4 | B_V2 | B_V3 | Ctrl_V2 |
+|:------------|-----:|-----:|--------:|--------:|-----:|-----:|--------:|
+| 8mS8sK~0150 | 3.85 | 3.76 |    3.37 |    3.55 |   NA |   NA |      NA |
+| DTCi0N~0734 |   NA | 4.28 |    4.07 |    4.21 | 4.37 | 4.35 |    4.06 |
+
+Per-sample intensities of proteins dropped by lm
+
+The missing cells (NA) explain why `lm` could not fit a full model for
+these proteins — they lack observations in one or more groups, so all
+coefficients cannot be estimated.
+
 ## Peptide-input facades
 
 The mixed-effects `lmer` facade and `ropeca` require lower-level

articles/ContrastFacade2Factor.html

@@ -253,7 +253,7 @@ sessionInfo()
     ##  [4] generics_0.1.4      tidyr_1.3.2         stringi_1.8.7      
     ##  [7] digest_0.6.39       magrittr_2.0.4      evaluate_1.0.5     
     ## [10] grid_4.5.2          RColorBrewer_1.1-3  fastmap_1.2.0      
-    ## [13] plyr_1.8.9          jsonlite_2.0.0      ggrepel_0.9.7      
+    ## [13] plyr_1.8.9          jsonlite_2.0.0      ggrepel_0.9.8      
     ## [16] limma_3.66.0        prolfqua_1.5.0      gridExtra_2.3      
     ## [19] httr_1.4.8          purrr_1.2.1         viridisLite_0.4.3  
     ## [22] scales_1.4.0        UpSetR_1.4.0        lazyeval_0.2.2     

articles/ContrastFacades.html

@@ -314,7 +314,7 @@ sessionInfo()
     ## 
     ## loaded via a namespace (and not attached):
     ##  [1] gtable_0.3.6        xfun_0.56           bslib_0.10.0       
-    ##  [4] htmlwidgets_1.6.4   ggrepel_0.9.7       lattice_0.22-7     
+    ##  [4] htmlwidgets_1.6.4   ggrepel_0.9.8       lattice_0.22-7     
     ##  [7] vctrs_0.7.1         tools_4.5.2         generics_0.1.4     
     ## [10] tibble_3.3.1        pkgconfig_2.0.3     Matrix_1.7-4       
     ## [13] pheatmap_1.0.13     data.table_1.18.2.1 RColorBrewer_1.1-3