ohofmann

arrayQualityMetrics(expressionset=msc.data,
                    outdir='report_raw',
                    force=TRUE,
                    do.logtransform=TRUE)

# Normalize and create second report
msc.eset <- call.exprs(msc.data, "rma");
arrayQualityMetrics(expressionset=msc.eset,
                    outdir='report_rma',
                    force=TRUE,

ohofmann

pdf('X_withDuplicates_labels.pdf', width=14, height=14)
plot(mdX, 
     pch=15,
     col=c(rgb(255, 0, 0, 100, maxColorValue=255), 
           rgb(0, 0, 255, 100, maxColorValue=255))[pData(lumiData)$Sex],
     cex=1.2)
text(mdX[, 1], mdX[, 2], labels=pData(lumiData)$SampleLabel, cex=.75)
dev.off()

ohofmann

# Plot correlation score in pairs() panel
panel.cor <- function(x, y, digits=2, prefix="", cex.cor)
{
  usr <- par("usr"); on.exit(par(usr))
  par(usr = c(0, 1, 0, 1))
  r = (cor(x, y, use="pairwise"))
  txt <- format(c(r, 0.123456789), digits=digits)[1]
  txt <- paste(prefix, txt, sep="")
  if(missing(cex.cor)) cex <- 0.6/strwidth(txt)
  text(0.5, 0.5, txt, cex=cex )

ohofmann

setwd('/Users/oho/Desktop/Methylation/')
load('probes.450k.rda')

data <- probes.450k

probes <- data$Probe_ID
length(probes)
bedMatrix <- matrix(nrow=length(probes), ncol=6)

for (i in 1:length(probes)) {

ohofmann

library(lumi)
library(arrayQualityMetrics)

setwd('~/Dropbox/Shared/Mike_LungCancer/')
data <- lumiR.batch(c('Batch1_EA10095_20101202_FinalReportNonNormNoBack.txt',
                      'Batch2_EA10095_20110729_FinalReportNonNormNoBack_clean.txt'),
                    sampleInfoFile='SampleDesc.txt')

png('density.png', width=1200, height=800)
density(data)

ohofmann

library(lumi)
library(arrayQualityMetrics)

setwd('D:/Storage/My Dropbox/Shared/Mike_LungCancer/')
#setwd('~/Dropbox/Shared/Mike_LungCancer/')
data <- lumiR.batch(c('Batch1_EA10095_20101202_FinalReportNonNormNoBack.txt',
                      'Batch2_EA10095_20110729_FinalReportNonNormNoBack_clean.txt'),
                    sampleInfoFile='SampleDesc.txt')

png('density.png', width=1200, height=800)

ohofmann

library(oligo)
library(genefilter)
library(RColorBrewer)
library(sva)
library(SpeCond)

basepath <- '/n/HSPH/projects/am_trap'

#
# Get array data

ohofmann

library(simpleaffy)
library(mouse430a2.db)
library(arrayQualityMetrics)
library(RColorBrewer)
library(pheatmap)

#library(pathprint)
#library(ggplot2)
#library(ggdendro)
#library("AnnotationDbi")

ohofmann

library(ReadqPCR)
library(NormqPCR)
library(pheatmap)
library(RColorBrewer)
library(ggplot2)

######################################################################
# Setup
######################################################################
# Pairwise correlations

ohofmann

# Start with basic quality controls from lumi, highlight
# samples by tissue information, also extract gender information
colors <- brewer.pal(3, 'Set1')
tissues <- pData(lumiData)$Tissue
gender <- pData(lumiData)$Sex

# Basic sample relations
pdf('sampleRelations_mds_0.1_withRedos.pdf')
plotSampleRelation(lumiData, method='mds', cv.Th=0.1, col=colors[tissues])
dev.off()