Mercurial > repos > fubar > differential_count_models

changeset 123:51f998262ada draft

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Uploaded
author fubar
date Tue, 25 Nov 2014 05:36:47 -0500
parents 6ded550dcc7d
children 731315bd6e48
files rgedgeRpaired_nocamera.xml
diffstat 1 files changed, 2 insertions(+), 1 deletions(-) [+]
line wrap: on
line diff
--- a/rgedgeRpaired_nocamera.xml	Sun Nov 23 07:18:05 2014 -0500
+++ b/rgedgeRpaired_nocamera.xml	Tue Nov 25 05:36:47 2014 -0500
@@ -546,7 +546,8 @@
   DGLM = glmFit(myDGEList,design=mydesign)
   DE = glmLRT(DGLM,coef=ncol(DGLM\$design)) # always last one - subject is first if needed
   efflib = myDGEList\$samples\$lib.size*myDGEList\$samples\$norm.factors
-  normData = (1e+06*myDGEList\$counts/efflib)
+  normData = cpm(myDGEList)
+  ### normData = (1e+06*myDGEList\$counts/efflib)
   uoutput = cbind( 
     Name=as.character(rownames(myDGEList\$counts)),
     DE\$table,