resolve merge conflict for limma confounder test.

zellerlab · May 10, 2024 · 6055aa1 · 6055aa1
2 parents 7c097b5 + 3c7ba22
commit 6055aa1
Showing 1 changed file with 3 additions and 14 deletions.
diff --git a/R/helper_tests.R b/R/helper_tests.R
@@ -613,21 +613,10 @@ test.via.limma <- function(data, label, conf){
   stopifnot(all(colnames(data)==names(label)))
   test.package('limma')
   if (is.null(conf)){
-    fit <- lmFit(data, design = model.matrix(~label))
-    res <- eBayes(fit)
-    p.val <- res$p.value[,'label']
+    fit <- lmFit(data, design = data.frame(intercept = -1, label))
   } else {
-    df <- model.matrix(~label+conf[colnames(data), 'conf'])
-    colnames(df)[1] <- 'intercept'
-    colnames(df)[3] <- 'conf'
-    df2 <- data.frame(label=label, conf=conf[colnames(data), 'conf'])
-    # fit <- lmFit(data, design = df) 
-    # contr <- makeContrasts(label-intercept, levels = colnames(df))
-    # contr.fit <- contrasts.fit(fit, contrasts = contr)
-    fit <- lmFit(data, design = data.frame(intercept = -1, label), 
-                 block=conf[colnames(data), 'conf'], correlation = 0.5)
-    res <- eBayes(fit)
-    p.val <- res$p.value[,'label']
+    x <- duplicateCorrelation(data, design = data.frame(label), block = conf[colnames(data), 'conf'])
+    fit <- lmFit(data, design = data.frame(intercept = -1, label), block = conf[colnames(data), 'conf'], correlation = x[[1]])
   }