Difference between revisions of "Microarray"
TaejoonKwon (Talk | contribs) (Created page with "* http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE12613 = exp.txt = <pre> Filename Sample Group Description CEL/GSM315919.CEL ICD1 ICD ICD-1 CEL/G...") |
(No difference)
|
Revision as of 10:30, 17 May 2014
exp.txt
Filename Sample Group Description CEL/GSM315919.CEL ICD1 ICD ICD-1 CEL/GSM315920.CEL ICD2 ICD ICD-2 CEL/GSM315921.CEL ICD3 ICD ICD-3 CEL/GSM315922.CEL FoxJ1_1 FoxJ1 ICD-FoxJ1-1 CEL/GSM315923.CEL FoxJ1_2 FoxJ1 ICD-FoxJ1-2
affy-RMA.R
Invalid language.
You need to specify a language like this: <source lang="html4strict">...</source>
Supported languages for syntax highlighting:
4cs, 6502acme, 6502kickass, 6502tasm, 68000devpac, abap, actionscript, actionscript3, ada, algol68, apache, applescript, apt_sources, arm, asm, asp, asymptote, autoconf, autohotkey, autoit, avisynth, awk, bascomavr, bash, basic4gl, bf, bibtex, blitzbasic, bnf, boo, c, c_loadrunner, c_mac, caddcl, cadlisp, cfdg, cfm, chaiscript, cil, clojure, cmake, cobol, coffeescript, cpp, cpp-qt, csharp, css, cuesheet, d, dcl, dcpu16, dcs, delphi, diff, div, dos, dot, e, ecmascript, eiffel, email, epc, erlang, euphoria, f1, falcon, fo, fortran, freebasic, freeswitch, fsharp, gambas, gdb, genero, genie, gettext, glsl, gml, gnuplot, go, groovy, gwbasic, haskell, haxe, hicest, hq9plus, html4strict, html5, icon, idl, ini, inno, intercal, io, j, java, java5, javascript, jquery, kixtart, klonec, klonecpp, latex, lb, ldif, lisp, llvm, locobasic, logtalk, lolcode, lotusformulas, lotusscript, lscript, lsl2, lua, m68k, magiksf, make, mapbasic, matlab, mirc, mmix, modula2, modula3, mpasm, mxml, mysql, nagios, netrexx, newlisp, nsis, oberon2, objc, objeck, ocaml, ocaml-brief, octave, oobas, oorexx, oracle11, oracle8, oxygene, oz, parasail, parigp, pascal, pcre, per, perl, perl6, pf, php, php-brief, pic16, pike, pixelbender, pli, plsql, postgresql, povray, powerbuilder, powershell, proftpd, progress, prolog, properties, providex, purebasic, pycon, pys60, python, q, qbasic, rails, rebol, reg, rexx, robots, rpmspec, rsplus, ruby, sas, scala, scheme, scilab, sdlbasic, smalltalk, smarty, spark, sparql, sql, stonescript, systemverilog, tcl, teraterm, text, thinbasic, tsql, typoscript, unicon, upc, urbi, uscript, vala, vb, vbnet, vedit, verilog, vhdl, vim, visualfoxpro, visualprolog, whitespace, whois, winbatch, xbasic, xml, xorg_conf, xpp, yaml, z80, zxbasic
library(affy) dataset_name <- 'GSE12613_foxj1' exp_table <- read.table(file="exp.txt",header=T,stringsAsFactors=FALSE,sep="\t") files_vector <- as.vector(exp_table$Filename,mode='character') samples_vector <- as.vector(exp_table$Sample,mode='character') affybatch_raw <- ReadAffy(filenames=files_vector,sampleNames=samples_vector) affybatch_corrected <- bg.correct(affybatch_raw, method='rma') affybatch_normalized <- normalize(affybatch_corrected, method='quantiles') eset_rma <- rma(affybatch_raw) write.exprs(eset_rma, file=paste(dataset_name,'.eset_rma.txt',sep=''))
affy-plot.R
Invalid language.
You need to specify a language like this: <source lang="html4strict">...</source>
Supported languages for syntax highlighting:
4cs, 6502acme, 6502kickass, 6502tasm, 68000devpac, abap, actionscript, actionscript3, ada, algol68, apache, applescript, apt_sources, arm, asm, asp, asymptote, autoconf, autohotkey, autoit, avisynth, awk, bascomavr, bash, basic4gl, bf, bibtex, blitzbasic, bnf, boo, c, c_loadrunner, c_mac, caddcl, cadlisp, cfdg, cfm, chaiscript, cil, clojure, cmake, cobol, coffeescript, cpp, cpp-qt, csharp, css, cuesheet, d, dcl, dcpu16, dcs, delphi, diff, div, dos, dot, e, ecmascript, eiffel, email, epc, erlang, euphoria, f1, falcon, fo, fortran, freebasic, freeswitch, fsharp, gambas, gdb, genero, genie, gettext, glsl, gml, gnuplot, go, groovy, gwbasic, haskell, haxe, hicest, hq9plus, html4strict, html5, icon, idl, ini, inno, intercal, io, j, java, java5, javascript, jquery, kixtart, klonec, klonecpp, latex, lb, ldif, lisp, llvm, locobasic, logtalk, lolcode, lotusformulas, lotusscript, lscript, lsl2, lua, m68k, magiksf, make, mapbasic, matlab, mirc, mmix, modula2, modula3, mpasm, mxml, mysql, nagios, netrexx, newlisp, nsis, oberon2, objc, objeck, ocaml, ocaml-brief, octave, oobas, oorexx, oracle11, oracle8, oxygene, oz, parasail, parigp, pascal, pcre, per, perl, perl6, pf, php, php-brief, pic16, pike, pixelbender, pli, plsql, postgresql, povray, powerbuilder, powershell, proftpd, progress, prolog, properties, providex, purebasic, pycon, pys60, python, q, qbasic, rails, rebol, reg, rexx, robots, rpmspec, rsplus, ruby, sas, scala, scheme, scilab, sdlbasic, smalltalk, smarty, spark, sparql, sql, stonescript, systemverilog, tcl, teraterm, text, thinbasic, tsql, typoscript, unicon, upc, urbi, uscript, vala, vb, vbnet, vedit, verilog, vhdl, vim, visualfoxpro, visualprolog, whitespace, whois, winbatch, xbasic, xml, xorg_conf, xpp, yaml, z80, zxbasic
dataset_name <- 'GSE12613_foxj1'
library(affy)
load( paste(dataset_name,'.affybatch_raw',sep='') )
load( paste(dataset_name,'.affybatch_normalized',sep='') )
load( paste(dataset_name,'.eset_rma',sep='') )
## Boxplot
png(filename=paste("plot/",dataset_name,".box_raw.png",sep=''),
width=1024,height=640);
par(mar=c(10,4,4,2))
boxplot( as.data.frame(log2(intensity(affybatch_raw))), las=2, mex=0.1,
main=paste(dataset_name,'(raw)',sep=''),
ylab="log2 intensity")
dev.off();
png(filename=paste("plot/",dataset_name,".box_rma.png", sep=''),
width=1024,height=640);
par(mar=c(10,4,4,2))
boxplot( as.data.frame(exprs(eset_rma)), las=2, mex=0.1,
main=paste(dataset_name,"(normalized - RMA)") )
dev.off();
## RMA, log2 intensity
rma_intensity <- as.data.frame(eset_rma);
rma_dist <- dist( as.matrix(rma_intensity) )
rma_clust <- hclust( rma_dist, method="average")
png(filename=paste("plot/",dataset_name,".rma_log_clust.png",sep=''),
width=1024,height=640);
## RMA, log2 Rank
rma_rank <- matrix(data=NA, nrow=nrow(eset_rma), ncol=ncol(eset_rma) );
nsample <- ncol(eset_rma)
for(i in 1:nsample) {
rma_rank[,i] <- rank(exprs(eset_rma[,i]) );
}
colnames(rma_rank) <- sampleNames(eset_rma)
rma_rank_dist <- dist( t(rma_rank) )
rma_rank_clust <- hclust(rma_rank_dist, method="average")
png(filename=paste("plot/",dataset_name,'.rma_rank_clust.png',sep=''),
width=1024, height=640);
plot(rma_rank_clust,
main=paste(dataset_name,":hclust_average(rma,log2_rank)",sep=''))
dev.off()
dataset_name <- 'GSE12613_foxj1'
library(affy)
library(affyPLM)
load( paste(dataset_name,'.affybatch_raw',sep='') )
affybatch_raw_PLM <- fitPLM(affybatch_raw)
sample_names <- sampleNames(affybatch_raw)
for(i in 1:length(sample_names)) {
filename_img <- paste(sample_names[i],".PLM_resids.png", sep="")
png(filename=filename_img, width=1024, height=1024);
image( affybatch_raw_PLM, which=i, type="resids", add.legend=TRUE )
dev.off()
}
png(filename=paste(dataset_name,'.RLE.png',sep=''),
width=1024,height=800)
par(mar=c(10,4,4,2))
RLE(affybatch_raw_PLM, fin=c(1024, 600), las=2, mex=0.1,
main=paste("Relative Log Expression(RLE) for ",dataset_name, sep=''))
dev.off()
