Changes between Version 8 and Version 9 of SOPs/normalize_ma

Timestamp:

10/08/13 15:46:09 (11 years ago)

Author:

byuan

Comment:

--

SOPs/normalize_ma

@@ -26 +26 @@
     arrayQualityMetrics(eset, outdir="QC", force=TRUE)
     
+    # arrayQualityMetrics using oligo package
+    library(arrayQualityMetrics)
+    library(oligo)
+    library(pd.huex.1.0.st.v2)
+    geneCELs =list.celfiles(full.names = TRUE)
+    affyGeneFS = read.celfiles(geneCELs)
+    eset.oligoGeneCore = rma(affyGeneFS, target = "core")
+    arrayQualityMetrics(eset.oligoGeneCore, outdir="QC", force=TRUE)
+
+
     #Agilent (arrayQualityMetrics) on 2-color
     library(arrayQualityMetrics)