Changes between Version 6 and Version 7 of SOPs/normalize_ma

Timestamp:

08/19/13 12:36:01 (11 years ago)

Author:

thiruvil

Comment:

--

SOPs/normalize_ma

@@ -77 +77 @@
     arrayQualityMetrics(eset, outdir="QC", force=TRUE)
 }}}
+ 
+  * Clustering samples after normalization can be used to see possible batch effects
+{{{
+    d=dist(t(eset.rma.expr))
+    plot(hclust(d, method="average"))
+}}}
+
+
   * Analysis of Mouse (or Human) Gene 1.0 ST Arrays
  The use of the Affy CDF file for these arrays is not recommended because it is "not supported" by Affymetrix. For these arrays use either a custom CDF (ex: CELs.entrez = ReadAffy(cdfname="mogene10stv1mmentrezgcdf")) or the standard Affymetrix probeset definitions but using the oligo package. The output from the oligo package agrees with the output from commercial Affymetrix analysis software.  '''NOTE: Normalizing these arrays with small sample size (eg. < 5) may not work properly or as expected, eg. normalized values might occur multiple times within, or across, arrays. Possible solutions may include:'''