[Robast-commits] r260 - in pkg/RobLoxBioC: R man

[noreply at r-forge.r-project.org]

Author: stamats
Date: 2009-03-04 09:58:34 +0100 (Wed, 04 Mar 2009)
New Revision: 260

Modified:
   pkg/RobLoxBioC/R/robloxAffyBatch.R
   pkg/RobLoxBioC/man/robloxbioc.Rd
Log:
added Affymetrix scale normalization

Modified: pkg/RobLoxBioC/R/robloxAffyBatch.R
===================================================================
--- pkg/RobLoxBioC/R/robloxAffyBatch.R	2009-03-03 08:00:21 UTC (rev 259)
+++ pkg/RobLoxBioC/R/robloxAffyBatch.R	2009-03-04 08:58:34 UTC (rev 260)
@@ -2,9 +2,9 @@
 ## Use robloxbioc to preprocess Affymetrix-data - comparable to MAS 5.0
 ###############################################################################
 setMethod("robloxbioc", signature(x = "AffyBatch"),
-    function(x, pmcorrect = "roblox", verbose = TRUE,
+    function(x, pmcorrect = "roblox", normalize = FALSE, verbose = TRUE,
             eps = NULL, eps.lower = 0, eps.upper = 0.1, steps = 1L, mad0 = 1e-4,
-            contrast.tau = 0.03, scale.tau = 10, delta = 2^(-20)) {
+            contrast.tau = 0.03, scale.tau = 10, delta = 2^(-20), sc = 500) {
         n <- length(x)
         ids <- featureNames(x)
         m <- length(ids)
@@ -57,7 +57,6 @@
                 l <- t(t(pps.mm >= pps.pm) & (sb[k,] <= contrast.tau))
                 pps.im[l] <- t(t(pps.pm)/2^(contrast.tau/(1 + (contrast.tau - sb[k,])/scale.tau)))[l]
                 pm.corrected <- pmax.int(pps.pm - pps.im, delta)
-    #            pm.corrected[pm.corrected < delta] <- delta
                 res[[k]] <- pm.corrected
             }
         }else{
@@ -83,5 +82,15 @@
         eset <- new("ExpressionSet", phenoData = phenoData(x), 
             experimentData = experimentData(x), exprs = exp.mat, 
             se.exprs = se.mat, annotation = annotation(x))
+        if(normalize){
+            if(verbose) cat("Scale normalization ...")
+            for (i in 1:ncol(exprs(eset))) {
+                slg <- exprs(eset)[, i]
+                sf <- sc/mean(slg, trim = 0.02)
+                reported.value <- sf * slg
+                exprs(eset)[, i] <- reported.value
+            }
+            if(verbose) cat(" done.\n")
+        }
         return(eset)
     })

Modified: pkg/RobLoxBioC/man/robloxbioc.Rd
===================================================================
--- pkg/RobLoxBioC/man/robloxbioc.Rd	2009-03-03 08:00:21 UTC (rev 259)
+++ pkg/RobLoxBioC/man/robloxbioc.Rd	2009-03-04 08:58:34 UTC (rev 260)
@@ -14,9 +14,9 @@
 
 \S4method{robloxbioc}{matrix}(x, eps = NULL, eps.lower = 0, eps.upper = 0.1, steps = 1L, mad0 = 1e-4)
 
-\S4method{robloxbioc}{AffyBatch}(x, pmcorrect = "roblox", verbose = TRUE,  
+\S4method{robloxbioc}{AffyBatch}(x, pmcorrect = "roblox", normalize = "FALSE", verbose = TRUE,  
                                  eps = NULL, eps.lower = 0, eps.upper = 0.1, steps = 1L, mad0 = 1e-4,
-                                 contrast.tau = 0.03, scale.tau = 10, delta = 2^(-20))
+                                 contrast.tau = 0.03, scale.tau = 10, delta = 2^(-20), sc = 500)
 }
 \arguments{
   \item{x}{ biological data. }
@@ -32,13 +32,15 @@
   \item{pmcorrect}{ method used for PM correction; so far only "roblox" and \code{pm.only} 
     are implemented. The algorithm is comparable to the algorithm of MAS 5.0; confer
     \code{\link[affy]{pmcorrect.mas}}. }
+  \item{normalize}{ logical: if \code{TRUE}, Affymetrix scale normalization is performed. }
+  \item{verbose}{ logical: if \code{TRUE}, some messages are printed. }
   \item{contrast.tau}{ a number denoting the contrast tau parameter; confer the MAS 5.0 
     PM correction algorithm. }
   \item{scale.tau}{ a number denoting the scale tau parameter; confer the MAS 5.0 
     PM correction algorithm. }
   \item{delta}{ a number denoting the delta parameter; confer the MAS 5.0 
     PM correction algorithm. }
-  \item{verbose}{ logical: if \code{TRUE}, some messages are printed }
+  \item{sc}{ value at which all arrays will be scaled to. }
 }
 \details{
   The optimally-robust resp. the radius-minimax (rmx) estimator for normal location 
@@ -118,6 +120,7 @@
 if(require(affydata)){
     data(Dilution)
     eset <- robloxbioc(Dilution)
+    eset1 <- robloxbioc(Dilution, normalize = TRUE)
 }
 }
 \concept{normal location and scale}