Changes between Version 32 and Version 33 of SOPs/rna-seq-diff-expressions

Timestamp:

09/20/16 11:50:45 (8 years ago)

Author:

thiruvil

Comment:

--

SOPs/rna-seq-diff-expressions

@@ -139 +139 @@
   Sample R code for reducing the date effect (old vs. new) is
 
- {{{
+    {{{
         target   <- read.delim("target.txt", header=T)
         genotype <- factor(target$genotype, levels=c("WT", "KO"))
@@ -153 +153 @@
         Fit <- glmFit(Y2, Design)
         Lrt <- glmLRT(Fit, coef="genotypeKO") # where 'coef' points to the column name in 'Design'
- }}}
+    }}}
 
   The data structure Lrt$table contains the values for log2FC (log 2 fold change) and p-value.
@@ -159 +159 @@
   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,
+    {{{
+    cpm.out=cpm(my.DGEList)
+    logCPM <- removeBatchEffect(cpm.out, batch=batch)  #where batch is based on your design
+    }}}
 
  * **Other**