[Robast-commits] r291 - in pkg/RobLoxBioC: R inst/scripts man
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Tue Apr 21 12:01:21 CEST 2009
Author: stamats
Date: 2009-04-21 12:01:21 +0200 (Tue, 21 Apr 2009)
New Revision: 291
Modified:
pkg/RobLoxBioC/R/robloxbiocAffyBatch.R
pkg/RobLoxBioC/R/robloxbiocMatrix.R
pkg/RobLoxBioC/inst/scripts/AffymetrixExample.R
pkg/RobLoxBioC/man/robloxbioc.Rd
Log:
some minor updates
Modified: pkg/RobLoxBioC/R/robloxbiocAffyBatch.R
===================================================================
--- pkg/RobLoxBioC/R/robloxbiocAffyBatch.R 2009-04-21 04:36:13 UTC (rev 290)
+++ pkg/RobLoxBioC/R/robloxbiocAffyBatch.R 2009-04-21 10:01:21 UTC (rev 291)
@@ -4,7 +4,7 @@
setMethod("robloxbioc", signature(x = "AffyBatch"),
function(x, bg.correct = TRUE, pmcorrect = TRUE, normalize = FALSE,
add.constant = 32, verbose = TRUE,
- eps = NULL, eps.lower = 0, eps.upper = 0.1, steps = 3L,
+ eps = NULL, eps.lower = 0, eps.upper = 0.05, steps = 3L,
fsCor = TRUE, mad0 = 1e-4, contrast.tau = 0.03, scale.tau = 10,
delta = 2^(-20), sc = 500) {
if(bg.correct){
Modified: pkg/RobLoxBioC/R/robloxbiocMatrix.R
===================================================================
--- pkg/RobLoxBioC/R/robloxbiocMatrix.R 2009-04-21 04:36:13 UTC (rev 290)
+++ pkg/RobLoxBioC/R/robloxbiocMatrix.R 2009-04-21 10:01:21 UTC (rev 291)
@@ -3,7 +3,7 @@
## matrix
###############################################################################
setMethod("robloxbioc", signature(x = "matrix"),
- function(x, eps = NULL, eps.lower = 0, eps.upper = 0.1, steps = 3L,
+ function(x, eps = NULL, eps.lower = 0, eps.upper = 0.05, steps = 3L,
fsCor = TRUE, mad0 = 1e-4){
stopifnot(is.numeric(x))
if(ncol(x) <= 2){
@@ -48,6 +48,8 @@
if(steps < 1)
stop("'steps' has to be some positive integer value")
steps <- as.integer(steps)
+ if(steps > 10)
+ warning("steps > 10 => numbers between 1 and 5 should be sufficient.")
mean <- rowMedians(x, na.rm = TRUE)
sd <- rowMedians(abs(x-mean), na.rm = TRUE)/qnorm(0.75)
Modified: pkg/RobLoxBioC/inst/scripts/AffymetrixExample.R
===================================================================
--- pkg/RobLoxBioC/inst/scripts/AffymetrixExample.R 2009-04-21 04:36:13 UTC (rev 290)
+++ pkg/RobLoxBioC/inst/scripts/AffymetrixExample.R 2009-04-21 10:01:21 UTC (rev 291)
@@ -89,7 +89,7 @@
table(minKD.hgu133a$n)
###########################################################
-## Comparison with normal samples
+## Comparison with normal (pseudo) random samples
###########################################################
## takes more than 90 min on Intel P9500 (64bit Linux, 4 GByte RAM)
@@ -130,7 +130,7 @@
legend("topright", legend = "minimal possible distance", fill = "orange")
#######################################
-## Figure 1 in Kohl and Deigner (2009)
+## Figure in Kohl and Deigner (2009)
#######################################
res1 <- split(as.vector(minKD.hgu95a$dist), as.vector(minKD.hgu95a$n))
res2 <- split(as.vector(minKD.hgu133a$dist), as.vector(minKD.hgu133a$n))
@@ -162,6 +162,7 @@
dev.off()
## Comparison of median distances
+## Table in Kohl and Deigner (2009)
round(sapply(res1, median) - sapply(res3, median), 4)
round(sapply(res2, median) - sapply(res3, median)[-c(1,2,4,7)], 4)
@@ -399,6 +400,9 @@
## Comparison plot
## hgu95a
affycomp.compfig5a(list(roblox.hgu95a$FC,
+ mas5.assessment$FC),
+ method.names = c("roblox", "MAS 5.0"))
+affycomp.compfig5a(list(roblox.hgu95a$FC,
roblox.hgu95a32$FC,
roblox.hgu95a.pmonly$FC,
roblox.hgu95a.pmonly32$FC,
@@ -408,12 +412,15 @@
"roblox + 32 (PM)", "MAS 5.0", "RMA"))
## hgu133a
+affycomp.compfig5a(list(roblox.hgu133a$FC,
+ mas5.assessment.133$FC),
+ method.names = c("roblox", "MAS 5.0"))
affycomp.compfig5a(list(roblox.hgu133a$FC,
roblox.hgu133a32$FC,
roblox.hgu133a.pmonly$FC,
roblox.hgu133a.pmonly32$FC,
- mas5.assessment$FC,
- rma.assessment$FC),
+ mas5.assessment.133$FC,
+ rma.assessment.133$FC),
method.names = c("roblox", "roblox + 32", "roblox (PM)",
"roblox + 32 (PM)", "MAS 5.0", "RMA"))
@@ -438,6 +445,9 @@
## Comparison plot
## hgu95a
+affycomp.compfig5b(list(roblox.hgu95a$FC,
+ mas5.assessment$FC),
+ method.names = c("roblox", "MAS 5.0"))
affycomp.compfig5b(list(roblox.hgu95a$FC,
roblox.hgu95a32$FC,
roblox.hgu95a.pmonly$FC,
@@ -448,12 +458,15 @@
"roblox + 32 (PM)", "MAS 5.0", "RMA"))
## hgu133a
+affycomp.compfig5b(list(roblox.hgu133a$FC,
+ mas5.assessment.133$FC),
+ method.names = c("roblox", "MAS 5.0"))
affycomp.compfig5b(list(roblox.hgu133a$FC,
roblox.hgu133a32$FC,
roblox.hgu133a.pmonly$FC,
roblox.hgu133a.pmonly32$FC,
- mas5.assessment$FC,
- rma.assessment$FC),
+ mas5.assessment.133$FC,
+ rma.assessment.133$FC),
method.names = c("roblox", "roblox + 32", "roblox (PM)",
"roblox + 32 (PM)", "MAS 5.0", "RMA"))
@@ -510,6 +523,8 @@
## Table
###############################################################################
## hgu95a
+tab.hgu95a <- tableAll(roblox.hgu95a, mas5.assessment)
+round(tab.hgu95a, 4)
tab.hgu95a <- tableAll(roblox.hgu95a, roblox.hgu95a32,
roblox.hgu95a.pmonly, roblox.hgu95a.pmonly32,
mas5.assessment, rma.assessment)
@@ -523,31 +538,34 @@
mas5.ass <- assessSpikeIn2(mas5.res, method.name = "MAS 5.0")
rma.ass <- assessSpikeIn2(rma.res, method.name = "RMA")
-## use vsn for normalization ...
-library(vsn)
-vsn.res <- vsn2(spikein.hgu95a)
-spikein.vsn <- spikein.hgu95a
-exprs(spikein.vsn) <- 2^exprs(vsn.res)
-vsn.roblox <- robloxbioc(spikein.vsn, bg.correct = FALSE, pmcorrect = FALSE,
- normalize = FALSE, add.constant = 32)
-vsn.roblox.log2 <- vsn.roblox
-exprs(vsn.roblox.log2) <- log2(exprs(vsn.roblox))
-vsn.rmx <- assessSpikeIn2(vsn.roblox.log2, method.name = "vsn+roblox")
-
+tab.hgu95a.2 <- tableAll(roblox.hgu95a.2, mas5.ass)
+round(tab.hgu95a.2, 4)
tab.hgu95a.2 <- tableAll(roblox.hgu95a.2, roblox.hgu95a32.2,
roblox.hgu95a.pmonly.2, roblox.hgu95a.pmonly32.2,
- mas5.ass, rma.ass, vsn.rmx)
-round(tab.hgu95a.2, 3)
+ mas5.ass, rma.ass)
+round(tab.hgu95a.2, 4)
## hgu133a
+tab.hgu133a <- tableAll(roblox.hgu133a, mas5.assessment.133)
+round(tab.hgu133a, 4)
tab.hgu133a <- tableAll(roblox.hgu133a, roblox.hgu133a32,
roblox.hgu133a.pmonly, roblox.hgu133a.pmonly32,
mas5.assessment.133, rma.assessment.133)
round(tab.hgu133a, 4)
+system.time(mas5.res.133 <- mas5(spikein.hgu133a))
+system.time(rma.res.133 <- rma(spikein.hgu133a))
+mas5.exprs <- exprs(mas5.res.133)
+exprs(mas5.res.133) <- log2(mas5.exprs)
+mas5.ass.133 <- assessSpikeIn2(mas5.res.133, method.name = "MAS 5.0")
+rma.ass.133 <- assessSpikeIn2(rma.res.133, method.name = "RMA")
+
+tab.hgu133a.2 <- tableAll(roblox.hgu133a.2, mas5.ass.133)
+round(tab.hgu133a.2, 4)
tab.hgu133a.2 <- tableAll(roblox.hgu133a.2, roblox.hgu133a32.2,
- roblox.hgu133a.pmonly.2, roblox.hgu133a.pmonly32.2)
+ roblox.hgu133a.pmonly.2, roblox.hgu133a.pmonly32.2,
+ mas5.ass.133, rma.ass.133)
round(tab.hgu133a.2, 4)
@@ -563,3 +581,32 @@
tab.hgu133a.small <- cbind(tab.hgu133a.small, "whatsgood" = c(1, 1, 1, 0, NA, 1, 0, NA, 0, 1, 1))
round(tab.hgu133a.small, 4)
+
+## Figure in Kohl and Deigner (2009)
+res.sd <- assessSpikeInSD(eset.hgu133a.log2)
+res.sd.133 <- assessSpikeInSD(eset.hgu133a.log2)
+res.sd.mas <- assessSpikeInSD(mas5.res)
+res.sd.mas.133 <- assessSpikeInSD(mas5.res.133)
+postscript(file = "AffyMeanSD.eps", height = 6, width = 9, paper = "special",
+ horizontal = TRUE)
+par(mfrow = c(1, 2))
+plot(res.sd.mas$xsmooth, res.sd.mas$ysmooth, type = "l", xlab = "mean log expression",
+ ylab = "mean SD", main = "HGU95A", lwd = 2, ylim = c(0, max(res.sd.mas$ysmooth)),
+ xlim = c(0, max(res.sd.mas$xsmooth)),
+ panel.first = abline(h = seq(0, 1.2, by = 0.2), v = c(0, 5, 10, 15), lty = 2, col = "grey"))
+lines(res.sd$xsmooth, res.sd$ysmooth, type = "l", lty = 2, lwd = 2)
+legend("topright", c("biweight", "rmx"), lty = 1:2, lwd = 2, bg = "white")
+plot(res.sd.133$xsmooth, res.sd.133$ysmooth, type = "l", lty = 2, lwd = 2,
+ xlab = "mean log expression", ylab = "mean SD", main = "HGU133A",
+ ylim = c(0, max(res.sd.mas$ysmooth)),
+ xlim = c(0, max(res.sd.133$xsmooth)),
+ panel.first = abline(h = seq(0, 1.2, by = 0.2), v = c(0, 5, 10, 15), lty = 2, col = "grey"))
+lines(res.sd.mas.133$xsmooth, res.sd.mas.133$ysmooth, type = "l", lwd = 2)
+legend("topright", c("biweight", "rmx"), lty = 1:2, lwd = 2, bg = "white")
+dev.off()
+
+
+## Table in Kohl and Deigner (2009)
+round(tableAll(roblox.hgu95a.2, mas5.ass)[c(1:3, 8:11),], 3)
+round(tableAll(roblox.hgu133a.2, mas5.ass.133)[c(1:3, 8:11),], 3)
+
Modified: pkg/RobLoxBioC/man/robloxbioc.Rd
===================================================================
--- pkg/RobLoxBioC/man/robloxbioc.Rd 2009-04-21 04:36:13 UTC (rev 290)
+++ pkg/RobLoxBioC/man/robloxbioc.Rd 2009-04-21 10:01:21 UTC (rev 291)
@@ -13,12 +13,12 @@
\usage{
robloxbioc(x, ...)
-\S4method{robloxbioc}{matrix}(x, eps = NULL, eps.lower = 0, eps.upper = 0.1, steps = 3L,
+\S4method{robloxbioc}{matrix}(x, eps = NULL, eps.lower = 0, eps.upper = 0.05, steps = 3L,
fsCor = TRUE, mad0 = 1e-4)
\S4method{robloxbioc}{AffyBatch}(x, bg.correct = TRUE, pmcorrect = TRUE, normalize = FALSE,
add.constant = 32, verbose = TRUE, eps = NULL,
- eps.lower = 0, eps.upper = 0.1, steps = 3L, fsCor = TRUE,
+ eps.lower = 0, eps.upper = 0.05, steps = 3L, fsCor = TRUE,
mad0 = 1e-4, contrast.tau = 0.03, scale.tau = 10,
delta = 2^(-20), sc = 500)
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