+
+# hard threshold
+thre <- 1.0 - fdr
+DEfound <- rownames(PP)[which(PP[, "PPDE"] >= thre)]
+
+results <- cbind(PP[DEfound, ], fc_res$PostFC[DEfound], fc_res$RealFC[DEfound])
+colnames(results) <- c("PPEE", "PPDE", "PostFC", "RealFC")
+write.table(results, file = paste(output_file, ".hard_threshold", sep = ""))
+
+# all
+results <- cbind(PP, fc_res$PostFC, fc_res$RealFC)
+colnames(results) <- c("PPEE", "PPDE", "PostFC", "RealFC")
+write.table(results, file = paste(output_file, ".all", sep = ""))