[Qpcr-commits] r116 - in pkg/NormqPCR: . R inst/doc

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

Author: jperkins
Date: 2010-09-01 18:54:09 +0200 (Wed, 01 Sep 2010)
New Revision: 116

Modified:
   pkg/NormqPCR/NAMESPACE
   pkg/NormqPCR/R/deltaDeltaCt.R
   pkg/NormqPCR/inst/doc/NormqPCR.Rnw
Log:
small bits


Modified: pkg/NormqPCR/NAMESPACE
===================================================================
--- pkg/NormqPCR/NAMESPACE	2010-06-15 23:16:53 UTC (rev 115)
+++ pkg/NormqPCR/NAMESPACE	2010-09-01 16:54:09 UTC (rev 116)
@@ -1,2 +1,2 @@
 importClasses(qPCRSet)
-export(geomMean,stabMeasureM,stabMeasureRho,selectHKs,deltaCt,replaceNAs,deltaDeltaCt,makeAllNAs,combineTechReps,replaceAboveCutOff, makeAllNAs, replaceNAs)
+export(geomMean,stabMeasureM,stabMeasureRho,selectHKs,deltaCt,replaceNAs,deltaDeltaCt,makeAllNAs,combineTechReps,replaceAboveCutOff,makeAllNAs,replaceNAs,plotDCt)

Modified: pkg/NormqPCR/R/deltaDeltaCt.R
===================================================================
--- pkg/NormqPCR/R/deltaDeltaCt.R	2010-06-15 23:16:53 UTC (rev 115)
+++ pkg/NormqPCR/R/deltaDeltaCt.R	2010-09-01 16:54:09 UTC (rev 116)
@@ -62,7 +62,8 @@
         } else if(! FALSE %in% is.na(VCase)) {
           warning("No Detector for Case")
           dCtCase <- rep(NA, length = VCase)
-          dCtControl <- NA
+#          dCtControl <- NA
+          sdCase <- NA
         } else {
           if(calc == "arith") {
             dCtCase <- mean(2^-(VCase - hkgVCase), na.rm=TRUE)
@@ -81,9 +82,12 @@
         if(length(VControl) == 1) {
           warning("Only one Detector for Control")
           dCtControl <- VControl
+          sdControl <- NA
         } else if(! FALSE %in% is.na(VControl)) {
           warning("No Detector for Control")
           dCtControl <- rep(NA, length = VControl)
+#          dCtCase <- NA
+          sdControl <- NA
         } else {
           if(calc == "arith") {
             dCtControl <- mean(2^-(VControl - hkgVControl), na.rm=TRUE)

Modified: pkg/NormqPCR/inst/doc/NormqPCR.Rnw
===================================================================
--- pkg/NormqPCR/inst/doc/NormqPCR.Rnw	2010-06-15 23:16:53 UTC (rev 115)
+++ pkg/NormqPCR/inst/doc/NormqPCR.Rnw	2010-09-01 16:54:09 UTC (rev 116)
@@ -218,8 +218,8 @@
 
 geNorm <- t(exprs(geNorm.qPCRBatch))
 
-tissue <- as.factor(c(rep("BM", 9), rep("POOL", 9), rep("FIB", 20), 
-                      rep("LEU", 13), rep("NB", 34)))
+tissue <- as.factor(c(rep("BM", 9),  rep("FIB", 20), rep("LEU", 13),
+                    rep("NB", 34), rep("POOL", 9)))
 res.BM <- selectHKs(geNorm[tissue == "BM",], method = "geNorm", 
                     Symbols = colnames(geNorm), minNrHK = 2, log = FALSE)
 res.POOL <- selectHKs(geNorm[tissue == "POOL",], method = "geNorm", 
@@ -275,7 +275,7 @@
 barplot(cbind(res.POOL$variation, res.LEU$variation, res.NB$variation, 
               res.FIB$variation, res.BM$variation), beside = TRUE, 
         col = mypalette, space = c(0, 2), 
-        names.arg = c("BM", "POOL", "FIB", "LEU", "NB"),
+        names.arg = c("POOL", "LEU", "NB", "FIB", "BM"),
         ylab = "Pairwise variation V",
         main = "Figure 3(a) in Vandesompele et al. (2002)")
 legend("topright", legend = c("V9/10", "V8/9", "V7/8", "V6/7",