fixed bug with inversion of test and reference conditions in edger_an…

…alysis.R
SnakeChunks · Sep 9, 2018 · 68dac76 · 68dac76
1 parent 70a9c99
commit 68dac76
Showing 1 changed file with 1 addition and 1 deletion.
diff --git a/scripts/RSnakeChunks/R/edger_analysis.R b/scripts/RSnakeChunks/R/edger_analysis.R
@@ -55,7 +55,7 @@ edger.analysis <- function(counts,
   ################################################################
   ## Detect differentially expressed genes by applying the exact
   ## negative binomial test from edgeR package.
-  edger.de <- exactTest(d, pair = c(test.condition, ref.condition), ...)      ## Run the exact negative binomial test
+  edger.de <- exactTest(d, pair = c(ref.condition, test.condition), ...)      ## Run the exact negative binomial test
 
   ## Sort genes by increasing p-values, i.e. by decreasing significance
   edger.tt <- topTags(edger.de, n = nrow(d), sort.by = "PValue")