Created
February 21, 2012 19:20
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Lumi normalization
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| 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) | |
| dev.off() | |
| data.T <- lumiT(data, method='log2', | |
| ifPlot=T, verbose=T) | |
| data.N <- lumiN(data.T) | |
| arrayQualityMetrics(data.N, | |
| outdir='log2_report') | |
| png('before_after.png', width=1600, height=2200) | |
| par(mfrow=c(2,1)) | |
| boxplot(exprs(data.T)) | |
| boxplot(exprs(data.N)) | |
| dev.off() |
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