1、Introduction to microarray data analysis with Bioconductor,Katherine S. Pollard March 11, 2004, Copyright 2004, all rights reserved,Bioconductor,Open source and open development R software project for the analysis and comprehension of biomedical and genomic data. Gene expression arrays (cDNA, Affyme
2、trix) Pathway graphs Genome sequence data Started in 2001 by Robert Gentleman, Dana Farber Cancer Institute. About 25 core developers, at various institutions in the US and Europe. Tools for integrating biological metadata from the web (annotation, literature) in the analysis of experimental data.,W
3、ebsites,Bioconductor: www.bioconductor.org software, data, and documentation; training materials from short courses; www.bioconductor.org/workshops/UCSC03/ucsc03.html mailing list. R: www.r-project.org software; documentation; RNews.,Basic R Commands,Working directory/file path: File Change dir setw
4、d(“C:/cygwin”)List objects in session: Misc List objects ls()Delete objects from session: Misc Remove all objects rm(my.matrix)Run a script: File Source R code source(“mycode.R”)Stopping R: File - Exit q(),Getting Help,Details about a specific command whose name you know (input arguments, options, a
5、lgorithm): ? t.test help(t.test) example(t.test) t.testInformation about commands containing a certain text string: apropos(“test”) help.search(“test”),Packages & Vignettes,Load a package library: Packages menu library(marrayTools)Run the package vignette: library(tkWidgets) vExplorer() openVignette
6、()Read the Vignette PDF fileLook at Short Courses and Lab Materials,Storing Data,Every R object (or the whole current working environment) can be stored into and restored from a file with the commands “save” and “load”. OR by using the File menu. save(x, file=“x.RData”) load(“x.RData”) save.image(“s
7、plicingArrays.RData”)These files are portable between MS-Windows, Unix, Mac versions of R.,Importing and Exporting Data,There are many ways to get data in and out. Most programs (e.g. Excel), as well as humans, know how to deal with rectangular tables in the form of tab-delimited text files. x write
8、.table(x, file=“x.txt”, sep=“t”)Also: write.matrix, write,Script to import GenePix data,library(marrayTools) importGPR-function(gal,details)g.info-read.marrayInfo(fname=gal,info.id=4:5,labels=5)a.info-read.marrayInfo(fname=details,labels=2)grid-read.marrayLayout(fname=gal,ngr=4,ngc=4,nsr=24,nsc=25,p
9、l.col=7,ctl.col=6)data-read.GenePix(layout=grid,targets=a.info,gnames=g.info,name.Gf=“F532 Median“,name.Rf=“F635 Median“)return(data) data.raw-importGPR(galfile,detailsfile),Note: If .gal file has n lines at top, before data begins, use skip=nNote: read.GenePix will read ALL .gpr files in current di
10、rectory. To read certain files (and to specify the order) use fname argument.,Working with log ratios,Loess normalization by print tip: data.norm-maNormMain(data.raw) ratios-as(data.norm,“exprSet“)Array statistics: apply(exprs(ratios),2,summary) apply(maGb(data.raw),2,median,na.rm=TRUE)Combine repli
11、cate spots on an array: meanM-aggregate(exprs(ratios), list(maLabels(maGnames(data.norm), mean, na.rm=TRUE)Export normalized log2 ratios: write.table(meanM,“Mvals.txt”,sep=“t”,row.names=F),Useful R/BioC Packages,Acknowledgments,Workshop materials developed withRobert Gentleman, HarvardSandrine Dudoi
12、t, UC Berkeley,Bioconductor core developers includeVince Carey, Harvard Yongchao Ge, Mount Sinai School of Medicine Robert Gentleman, Harvard Jeff Gentry, Dana-Farber Cancer Institute Rafael Irizarry, Johns Hopkins Yee Hwa (Jean) Yang, UCSF Jianhua (John) Zhang, Dana-Farber Cancer Institute Sandrine Dudoit, UC Berkeley,
