Mercurial > repos > yhoogstrate > edger_with_design_matrix

changeset 38:47eadcd9e4b8 draft

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Uploaded
author yhoogstrate
date Thu, 22 May 2014 10:14:59 -0400
parents 00b9ceac4332
children 1b8ecb48f6e7
files edgeR_Differential_Gene_Expression.xml
diffstat 1 files changed, 3 insertions(+), 2 deletions(-) [+]
line wrap: on
line diff
--- a/edgeR_Differential_Gene_Expression.xml	Thu May 22 10:10:03 2014 -0400
+++ b/edgeR_Differential_Gene_Expression.xml	Thu May 22 10:14:59 2014 -0400
@@ -280,9 +280,10 @@
     
     if(output_heatmap_plot != "/dev/null") {
       pdf(output_heatmap_plot)
-      etable2 <- topTags(lrt, n=100)\$table
+      etable2 <- topTags(lrt, n=100)$table
       order <- rownames(etable2)
-      heatmap(t(cpm(dge,normalized.lib.sizes=TRUE),sep="\t",row.names=TRUE,col.names=NA),log=TRUE))
+      cpm_sub <- cpm(dge,normalized.lib.sizes=TRUE,log=TRUE)[as.numeric(order),]
+      heatmap(t(cpm_sub))
       dev.off()
     }
   }