Replaced a basic volcano with the matrix volcano

jasonwalker80 · jasonwalker80 · commit 26515f2f820a · 2015-11-15T19:06:44.000-06:00
diff --git a/scripts/Tutorial_Module4_Part2_cummeRbund.R b/scripts/Tutorial_Module4_Part2_cummeRbund.R
@@ -56,9 +56,13 @@ m<-MAplot(genes(cuff),"UHR","HBR")
 m
 
 # Plot #5 - A volcano plot of p-value and fold_change per sample
-v<-csVolcano(genes(cuff),"UHR","HBR",alpha=0.05)
+#v<-csVolcano(genes(cuff),"UHR","HBR",alpha=0.05)
+#v
+# Replaced above with the matrix volcano view
+v<-csVolcanoMatrix(genes(cuff))
 v
 
+
 # Plot #6 - Using k-means clustering a dendrogram of the distance between sample replicates
 dend.rep<-csDendro(genes(cuff),replicates=T)
 

Original file line number	Diff line number	Diff line change
`@@ -56,9 +56,13 @@ m<-MAplot(genes(cuff),"UHR","HBR")`
`56`	`56`	`m`
`57`	`57`
`58`	`58`	`# Plot #5 - A volcano plot of p-value and fold_change per sample`
`59`		`-v<-csVolcano(genes(cuff),"UHR","HBR",alpha=0.05)`
	`59`	`+#v<-csVolcano(genes(cuff),"UHR","HBR",alpha=0.05)`
	`60`	`+#v`
	`61`	`+# Replaced above with the matrix volcano view`
	`62`	`+v<-csVolcanoMatrix(genes(cuff))`
`60`	`63`	`v`
`61`	`64`
	`65`	`+`
`62`	`66`	`# Plot #6 - Using k-means clustering a dendrogram of the distance between sample replicates`
`63`	`67`	`dend.rep<-csDendro(genes(cuff),replicates=T)`
`64`	`68`