Oliver Hofmann ohofmann
ohofmann
/ gist:2344582
Created
April 9, 2012 16:30
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| library(oligo) | |
| library(genefilter) | |
| library(RColorBrewer) | |
| library(sva) | |
| library(SpeCond) | |
| basepath <- '/n/HSPH/projects/am_trap' | |
| # | |
| # Get array data |
ohofmann
/ gist:1897630
Created
February 24, 2012 04:25
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| 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) |
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| 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:1836930
Created
February 15, 2012 16:03
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| setwd('/Users/oho/Desktop/Methylation/') | |
| load('probes.450k.rda') | |
| data <- probes.450k | |
| probes <- data$Probe_ID | |
| length(probes) | |
| bedMatrix <- matrix(nrow=length(probes), ncol=6) | |
| for (i in 1:length(probes)) { |
ohofmann
/ gist:1724594
Created
February 2, 2012 17:06
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| # Plot correlation score in pairs() panel | |
| panel.cor <- function(x, y, digits=2, prefix="", cex.cor) | |
| { | |
| usr <- par("usr"); on.exit(par(usr)) | |
| par(usr = c(0, 1, 0, 1)) | |
| r = (cor(x, y, use="pairwise")) | |
| txt <- format(c(r, 0.123456789), digits=digits)[1] | |
| txt <- paste(prefix, txt, sep="") | |
| if(missing(cex.cor)) cex <- 0.6/strwidth(txt) | |
| text(0.5, 0.5, txt, cex=cex ) |
ohofmann
/ gist:1717966
Created
February 1, 2012 16:47
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| pdf('X_withDuplicates_labels.pdf', width=14, height=14) | |
| plot(mdX, | |
| pch=15, | |
| col=c(rgb(255, 0, 0, 100, maxColorValue=255), | |
| rgb(0, 0, 255, 100, maxColorValue=255))[pData(lumiData)$Sex], | |
| cex=1.2) | |
| text(mdX[, 1], mdX[, 2], labels=pData(lumiData)$SampleLabel, cex=.75) | |
| dev.off() |
ohofmann
/ gist:1714547
Created
February 1, 2012 02:07
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| 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, |
NewerOlder