finished var transform section, now on to dim reduction and clustering

graphics_bioinf.R

@@ -304,7 +304,13 @@ counts_norm_crc_mat <- select(counts_crc_tidy, sample_id, ensembl_id, count_norm
                          as.matrix() 
 
 meanSdPlot(counts_norm_crc_mat)$gg +
-  ylim(c(0, 10))
+  ylim(c(0, 2000)) 
+
+
+## ----varStabCountData----------------------------------------------------
+counts_norm_trans_crc <- varianceStabilizingTransformation(counts_crc)
+meanSdPlot(counts_norm_trans_crc)$gg +
+  ylim(c(0, 5)) 
 
 ## ----session_info, cache = FALSE-----------------------------------------
 sessionInfo()