Changes between Version 56 and Version 57 of SOPs/rna-seq-diff-expressions

Timestamp:

02/20/18 12:59:15 (7 years ago)

Author:

gbell

Comment:

--

SOPs/rna-seq-diff-expressions

@@ -212 +212 @@
   Detailed information can be found in the [[http://www.bioconductor.org/packages/release/bioc/vignettes/edgeR/inst/doc/edgeRUsersGuide.pdf|edgeR User Guide]] (after a search for "batch effects").
 
-    * To print out batch-effect corrected CPM values, a possible option is outlined in this following SEQanswers post, [[http://seqanswers.com/forums/showthread.php?t=26923 | EdgeR cpm values after batch effects]], reply from Gordon Smyth,
+    * To print out batch-effect corrected CPM or other normalized values from DESeq, DESeq2, or edgeR, one can use the limma removeBatchEffect() command 
     {{{
-    cpm.out=cpm(my.DGEList)
     # Input needs to be log-transformed values
     logCPM <- removeBatchEffect(log2(cpm.out), batch=batch)  #where batch is based on your design