Oliver Hofmann ohofmann
ohofmann
/ gist:1714547
Created
February 1, 2012 02:07
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| 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
/ gist:1717966
Created
February 1, 2012 16:47
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| 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
/ gist:1724594
Created
February 2, 2012 17:06
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| # 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
/ gist:1836930
Created
February 15, 2012 16:03
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| 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)) { |
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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) |
ohofmann
/ gist:1897630
Created
February 24, 2012 04:25
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| 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
/ gist:2344582
Created
April 9, 2012 16:30
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| library(oligo) | |
| library(genefilter) | |
| library(RColorBrewer) | |
| library(sva) | |
| library(SpeCond) | |
| basepath <- '/n/HSPH/projects/am_trap' | |
| # | |
| # Get array data |
ohofmann
/ gist:2433005
Created
April 21, 2012 00:55
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| library(simpleaffy) | |
| library(mouse430a2.db) | |
| library(arrayQualityMetrics) | |
| library(RColorBrewer) | |
| library(pheatmap) | |
| #library(pathprint) | |
| #library(ggplot2) | |
| #library(ggdendro) | |
| #library("AnnotationDbi") |
ohofmann
/ gist:2433014
Created
April 21, 2012 01:00
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| library(ReadqPCR) | |
| library(NormqPCR) | |
| library(pheatmap) | |
| library(RColorBrewer) | |
| library(ggplot2) | |
| ###################################################################### | |
| # Setup | |
| ###################################################################### | |
| # Pairwise correlations |
ohofmann
/ gist:2771491
Created
May 22, 2012 20:41
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| # 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() |
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