Changes between Version 2 and Version 3 of SOPs/normalize_ma

Timestamp:

02/21/13 14:43:14 (12 years ago)

Author:

thiruvil

Comment:

--

SOPs/normalize_ma

@@ -133 +133 @@
   * Some custom CDF files are designed to define each gene by just one probeset, eliminating the issue of summarizing a gene represented by multiple probesets.
 
- Sample code for processing Affymetrix arrays using custom probeset definitions (CDF):
-
-{{{
+ Sample code for processing Affymetrix arrays using custom probeset definitions (CDF) and RMA:
+{{{
+    library(affy)
     library(hgu133plus2hsentrezgcdf)
     # Read all CEL files
@@ -141 +141 @@
     # Normalize with RMA or use justRMA for large data set
     eset = rma(CELs)
+    # Get the expression values alone (as a matrix)
+    eset.rma.expr = exprs(eset)
+}}}
+
+ Sample code for processing Affymetrix arrays using custom probeset definitions (CDF) and GCRMA:
+{{{
+    library(gcrma)
+    # Normalize with GCRMA where CEL files are in the directory CEL_Files
+    eset = justGCRMA(celfile.path = "CEL_Files", verbose=T, cdfname="mouse4302mmentrez")
     # Get the expression values alone (as a matrix)
     eset.rma.expr = exprs(eset)