Merge pull request #208 from bigomics/fix-fitFDistRobustly

set robust=FALSE limma::eBayes if needed (var<=0)
bigomics · Jan 14, 2025 · 023bb81 · 023bb81
2 parents 677ef15 + 722679d
commit 023bb81
Showing 1 changed file with 5 additions and 1 deletion.
diff --git a/R/gset-meta.r b/R/gset-meta.r
@@ -529,7 +529,11 @@ gset.fitContrastsWithLIMMA <- function(gsetX, contr.matrix, design,
     message("fitting gset.LIMMA contrasts with design matrix... ")
     vfit <- limma::lmFit(gsetX, design)
     vfit <- limma::contrasts.fit(vfit, contrasts = contr.matrix)
-    efit <- limma::eBayes(vfit, trend = trend, robust = TRUE)
+    ## efit <- limma::eBayes(vfit, trend = trend, robust = TRUE)
+    efit <- try({ limma::eBayes(vfit, trend = trend, robust = TRUE) })
+    if ("try-error" %in% class(efit)) {
+      efit <- limma::eBayes(vfit, trend = trend, robust = FALSE)
+    }
 
     tables <- list()
     i <- 1