<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en"
lang="en">
<head>
<meta http-equiv="Content-Type"
content="text/html;charset=utf-8" />
<title>
document_view
—
bioconductor.org
</title>
<base href="" />
<meta name="generator" content="Plone - http://plone.org" />
<meta content="sfadmin" name="DC.creator" />
<meta content="2006-10-10 13:24:00"
name="DC.date.created" />
<meta content="2006-10-10 13:24:00"
name="DC.date.modified" />
<meta content="Document" name="DC.type" />
<meta content="text/plain" name="DC.format" />
<!-- Basic crude style for Netscape4.x - This can be removed
if you don't want the special NS4 look - it will still work,
just be plain text instead. Column layout for Netscape4.x included -->
<link rel="Stylesheet" type="text/css"
href="../../../../../ploneNS4.css" />
<!-- Column style sheet. -->
<style type="text/css" media="screen"><!-- @import url(http://bioconductor.org/ploneColumns.css); --></style>
<!-- Main style sheets for CSS2 capable browsers -->
<style type="text/css" media="screen"><!-- @import url(http://bioconductor.org/plone.css); --></style>
<!-- Old style sheet from Plone 1.0, remove tal:condition="nothing" if you need to use the old styles.
Will be removed in Plone 2.1. -->
<!-- Alternate style sheets for the bigger/smaller text switcher -->
<link rel="alternate stylesheet" type="text/css"
media="screen"
href="../../../../../ploneTextSmall.css"
title="Small Text" />
<link rel="alternate stylesheet" type="text/css"
media="screen"
href="../../../../../ploneTextLarge.css"
title="Large Text" />
<!-- Style sheet used for printing -->
<link rel="stylesheet" type="text/css" media="print"
href="../../../../../plonePrint.css" />
<!-- Style sheet used for presentations (Opera is the only browser supporting this at the moment) -->
<link rel="stylesheet" type="text/css"
media="projection"
href="../../../../../plonePresentation.css" />
<!-- Internet Explorer CSS Fixes -->
<!--[if IE]>
<style type="text/css" media="all">@import url(http://bioconductor.org/ploneIEFixes.css);</style>
<![endif]-->
<!-- Custom style sheet if available -->
<style type="text/css" media="all"><!-- @import url(http://bioconductor.org/ploneCustom.css); --></style>
<link rel="shortcut icon"
href="../../../../../favicon.ico"
type="image/x-icon" />
<link rel="search"
href="../../../../../search_form"
title="Search this site" />
<link rel="up"
href="../Affy.1"
title="Up one level" />
<!-- Disable IE6 image toolbar -->
<meta http-equiv="imagetoolbar" content="no" />
<!-- A slot where you can insert CSS in the header from a template -->
<!-- min-width support for IE via Javascript, required for tableless -->
<!--[if IE]>
<script type="text/javascript"
src="http://bioconductor.org/plone_minwidth.js"></script>
<![endif]-->
<!-- A slot where you can insert elements in the header from a template -->
<!-- A slot where you can insert javascript in the header from a template -->
<!-- Common Plone ECMAScripts -->
<!-- Pull-down ECMAScript menu, only active if logged in -->
<!-- old google analytics here -->
<!-- Define dynamic server-side variables for javascripts in this one -->
<script type="text/javascript"
src="../../../../../plone_javascript_variables.js">
</script>
<script type="text/javascript"
src="../../../../../plone_javascripts.js">
</script>
<!-- Old JS from Plone 1.0, remove tal:condition="nothing" if you need to use the old pop-ups.
Will be removed in Plone 2.1 -->
</head>
<body class="section-workshops">
<div id="visual-portal-wrapper">
<div id="portal-top">
<a href="AffyLab-lab.R#documentContent" class="hiddenStructure">Skip to content.</a>
<h1 id="portal-logo">
<a href="../../../../../index.html">bioconductor.org</a>
</h1>
<div id="portal-slogan"><p>Bioconductor is an open source and open development software project<br />
for the analysis and comprehension of genomic data.</p></div>
<h5 class="hiddenStructure">Sections</h5>
<ul id="portal-globalnav"><li id="portaltab-index_html"
class="plain"><a href="../../../../../index.html"
accesskey="t">Home</a></li><li
id="portaltab-GettingStarted" class="plain"><a
href="../../../../../GettingStarted"
accesskey="t">Getting Started</a></li><li
id="portaltab-overview" class="plain"><a
href="../../../../../overview" accesskey="t">Overview</a></li><li
id="portaltab-download" class="plain"><a
href="../../../../../download" accesskey="t">Downloads</a></li><li
id="portaltab-docs" class="plain"><a
href="../../../../../docs" accesskey="t">Documentation</a></li><li
id="portaltab-biocpub" class="plain"><a
href="../../../../../pub" accesskey="t">Publications</a></li><li
id="portaltab-workshops" class="selected"><a
href="../../../../../workshops" accesskey="t">Workshops</a></li><li
id="portaltab-cabig" class="plain"><a
href="http://wiki.fhcrc.org/caBioc" accesskey="t">caBIG</a></li></ul>
</div>
<div class="visualClear"></div>
<!-- The wrapper div. It contains the three columns. -->
<div id="portal-columns" class="visualColumnHideNone">
<!-- start of the main and left columns -->
<div id="visual-column-wrapper">
<!-- start of main content block -->
<div id="portal-column-content" class="topmargin1">
<div id="content" class="">
<div class="documentContent" id="region-content">
<a name="documentContent"></a>
<h1 class="documentFirstHeading">AffyLab-lab.R</h1>
<div class="documentDescription"></div>
<div class="plain">
<p>###################################################
### chunk number 1: loadaffy
###################################################
library("affy")</p>
<p>###################################################
### chunk number 2: ReadAffy eval=FALSE
###################################################
## MyData <- ReadAffy()</p>
<p>###################################################
### chunk number 3: ReadAffy2 eval=FALSE
###################################################
## ReadAffy(filenames=filenames.of.your.data)</p>
<p>###################################################
### chunk number 4: readdata
###################################################
library("SpikeInSubset")
data(spikein95)
## There's a problem with the name of the annotation data
## so we fix it here. Normally, this should not be needed.
spikein95@cdfName <- "hgu95av2"</p>
<p>###################################################
### chunk number 5: addPhenoData
###################################################
pd <- data.frame(population=factor(c("Pop1", "Pop1", "Pop1",
"Pop2", "Pop2", "Pop2")),
replicate=c(1, 2, 3, 1, 2, 3))
rownames(pd) <- sampleNames(spikein95)
vl <- list(population="Pop1 is control, Pop2 is treatment",
replicate="1, 2, 3, arbitrary numbering")
phenoData(spikein95) <- new("phenoData", pData=pd, varLabels=vl)</p>
<p>###################################################
### chunk number 6: rma
###################################################
eset <- rma(spikein95)</p>
<p>###################################################
### chunk number 7: justrma eval=FALSE
###################################################
## eset<- just.rma(filenames=list.celfiles())</p>
<p>###################################################
### chunk number 8: exprsDemo
###################################################
e <- exprs(eset)
dim(e)</p>
<p>###################################################
### chunk number 9:
###################################################
pData(eset)
pData(spikein95)</p>
<p>###################################################
### chunk number 10: columnAccess
###################################################
Index1 <- which(eset$population == "Pop1")
Index2 <- which(eset$population == "Pop2")</p>
<p>###################################################
### chunk number 11: gcrma
###################################################
library("gcrma")
eset2 <- gcrma(spikein95)</p>
<p>###################################################
### chunk number 12: threestep
###################################################
library("affyPLM")
eset3 <- threestep(spikein95, background=FALSE,
summary.method="tukey.biweight")</p>
<p>###################################################
### chunk number 13: rowM
###################################################
d <- rowMeans(e[, Index2]) - rowMeans(e[, Index1])</p>
<p>###################################################
### chunk number 14: rowMeans
###################################################
a <- rowMeans(e)</p>
<p>###################################################
### chunk number 15: rowttests
###################################################
library("genefilter")
tt <- rowttests(eset, "population")</p>
<p>###################################################
### chunk number 16: eBayesEx
###################################################
library("limma")
design <- model.matrix(~eset$population)
fit <- lmFit(eset, design)
ebayes <- eBayes(fit) </p>
<p>###################################################
### chunk number 17: volcano
###################################################
lod <- -log10(tt$p.value)</p>
<p>plot(d, lod, cex=.25,
main="Volcano plot for $t$-test")
abline(h=2)</p>
<p>###################################################
### chunk number 18:
###################################################
table(tt$p.value<=0.01)</p>
<p>###################################################
### chunk number 19: toptable
###################################################
tab <- topTable(ebayes,coef=2,adjust.method="BH",n=10)
genenames <- as.character(tab$ID)</p>
<p>###################################################
### chunk number 20: annotate1
###################################################
library("annotate")</p>
<p>###################################################
### chunk number 21: annotate2
###################################################
annotation(eset)</p>
<p>###################################################
### chunk number 22: annotate3
###################################################
library("hgu95av2")</p>
<p>###################################################
### chunk number 23: entrezGeneAndSybol
###################################################
ll <- getLL(genenames, "hgu95av2")
sym <- getSYMBOL(genenames, "hgu95av2")</p>
<p>###################################################
### chunk number 24: output
###################################################
tab <- data.frame(sym, signif(tab<a href="#ref,-1">[,-1]</a>, 3))
htmlpage(ll, filename="GeneList1.html",
title="HTML report",
othernames=tab,
table.head=c("Locus ID",colnames(tab)), table.center=TRUE)</p>
<p>###################################################
### chunk number 25:
###################################################
browseURL("GeneList1.html")</p>
<p>###################################################
### chunk number 26:
###################################################
library("KEGG")
library("GO")
library("annaffy")
atab <- aafTableAnn(genenames, "hgu95av2",
aaf.handler())
saveHTML(atab, file="GeneList2.html") </p>
<p>###################################################
### chunk number 27: annaffy2
###################################################
aaf.handler()
atab <- aafTableAnn(genenames, "hgu95av2", aaf.handler()[c(2,5,8,12)])
saveHTML(atab, file="GeneList3.html")</p>
</div>
<div class="discussion">
</div>
</div>
</div>
</div>
<!-- end of main content block -->
<!-- start of the left (by default at least) column -->
<div id="portal-column-one">
<div class="visualPadding"> <br><br><br>
<!-- disabled left slot image <img tal:replace="structure nocall:here/pict.jpg" /> -->
<div class="portlet" id="portlet-navigation-tree">
<div>
<h5>Navigation</h5>
<div class="portletBody">
<div class="portletContent odd">
<a href="../../../../../GettingStarted/index.html"
accesskey="n"
class="navItem navLevel1"
title="">
<!-- Disable Folder icon
<img src="" height="16" width="16" alt=""
class="navIcon"
tal:condition="not:isAnon"
tal:attributes="src python:portal_url+'/'+sibling.getIcon(1);
title sibling/Type;" />
-->
<span class="navItemText">Getting Started</span>
</a>
<a href="../../../../../overview/index.html"
accesskey="n"
class="navItem navLevel1"
title="">
<!-- Disable Folder icon
<img src="" height="16" width="16" alt=""
class="navIcon"
tal:condition="not:isAnon"
tal:attributes="src python:portal_url+'/'+sibling.getIcon(1);
title sibling/Type;" />
-->
<span class="navItemText">Overview</span>
</a>
<a href="../../../../../download/index.html"
accesskey="n"
class="navItem navLevel1"
title="">
<!-- Disable Folder icon
<img src="" height="16" width="16" alt=""
class="navIcon"
tal:condition="not:isAnon"
tal:attributes="src python:portal_url+'/'+sibling.getIcon(1);
title sibling/Type;" />
-->
<span class="navItemText">Downloads</span>
</a>
<a href="../../../../../docs/index.html"
accesskey="n"
class="navItem navLevel1"
title="">
<!-- Disable Folder icon
<img src="" height="16" width="16" alt=""
class="navIcon"
tal:condition="not:isAnon"
tal:attributes="src python:portal_url+'/'+sibling.getIcon(1);
title sibling/Type;" />
-->
<span class="navItemText">Documentation</span>
</a>
<a href="../../../../../pub/index.html"
accesskey="n"
class="navItem navLevel1"
title="">
<!-- Disable Folder icon
<img src="" height="16" width="16" alt=""
class="navIcon"
tal:condition="not:isAnon"
tal:attributes="src python:portal_url+'/'+sibling.getIcon(1);
title sibling/Type;" />
-->
<span class="navItemText">Publications</span>
</a>
<a href="../../../../index.html"
accesskey="n"
class="navItem navLevel1"
title="">
<!-- Disable Folder icon
<img src="" height="16" width="16" alt=""
class="navIcon"
tal:condition="not:isAnon"
tal:attributes="src python:portal_url+'/'+sibling.getIcon(1);
title sibling/Type;" />
-->
<span class="navItemText">Workshops</span>
</a>
<a href="../../../../2010/index.html"
accesskey="n"
class="navItem navLevel2"
title="">
<!-- Disable Folder icon
<img src="" height="16" width="16" alt=""
class="navIcon"
tal:condition="not:isAnon"
tal:attributes="src python:portal_url+'/'+sibling.getIcon(1);
title sibling/Type;" />
-->
<span class="navItemText">2010</span>
</a>
<a href="../../../../2009/index.html"
accesskey="n"
class="navItem navLevel2"
title="">
<!-- Disable Folder icon
<img src="" height="16" width="16" alt=""
class="navIcon"
tal:condition="not:isAnon"
tal:attributes="src python:portal_url+'/'+sibling.getIcon(1);
title sibling/Type;" />
-->
<span class="navItemText">2009</span>
</a>
<a href="../../../../2008/index.html"
accesskey="n"
class="navItem navLevel2"
title="">
<!-- Disable Folder icon
<img src="" height="16" width="16" alt=""
class="navIcon"
tal:condition="not:isAnon"
tal:attributes="src python:portal_url+'/'+sibling.getIcon(1);
title sibling/Type;" />
-->
<span class="navItemText">2008</span>
</a>
<a href="../../../../2007/index.html"
accesskey="n"
class="navItem navLevel2"
title="">
<!-- Disable Folder icon
<img src="" height="16" width="16" alt=""
class="navIcon"
tal:condition="not:isAnon"
tal:attributes="src python:portal_url+'/'+sibling.getIcon(1);
title sibling/Type;" />
-->
<span class="navItemText">2007</span>
</a>
<a href="../../../index.html"
accesskey="n"
class="navItem navLevel2"
title="">
<!-- Disable Folder icon
<img src="" height="16" width="16" alt=""
class="navIcon"
tal:condition="not:isAnon"
tal:attributes="src python:portal_url+'/'+sibling.getIcon(1);
title sibling/Type;" />
-->
<span class="navItemText">2006</span>
</a>
<a href="../../index.html"
accesskey="n"
class="navItem navLevel3"
title="">
<!-- Disable Folder icon
<img src="" height="16" width="16" alt=""
class="navIcon"
tal:condition="not:isAnon"
tal:attributes="src python:portal_url+'/'+sibling.getIcon(1);
title sibling/Type;" />
-->
<span class="navItemText">R/Bioc Intro Course - October</span>
</a>
<a href="../index.html"
accesskey="n"
class="navItem navLevel4"
title="">
<!-- Disable Folder icon
<img src="" height="16" width="16" alt=""
class="navIcon"
tal:condition="not:isAnon"
tal:attributes="src python:portal_url+'/'+sibling.getIcon(1);
title sibling/Type;" />
-->
<span class="navItemText">labs</span>
</a>
<a href="../cDNA/index.html"
accesskey="n"
class="navItem navLevel5"
title="">
<!-- Disable Folder icon
<img src="" height="16" width="16" alt=""
class="navIcon"
tal:condition="not:isAnon"
tal:attributes="src python:portal_url+'/'+sibling.getIcon(1);
title sibling/Type;" />
-->
<span class="navItemText">cDNA (Two Color) Microarray</span>
</a>
<a href="index.html"
accesskey="n"
class="navItem navLevel5 currentNavItem"
title="">
<!-- Disable Folder icon
<img src="" height="16" width="16" alt=""
class="navIcon"
tal:condition="not:isAnon"
tal:attributes="src python:portal_url+'/'+sibling.getIcon(1);
title sibling/Type;" />
-->
<span class="navItemText">Affy</span>
</a>
<a href="../../../BioC2006/index.html"
accesskey="n"
class="navItem navLevel3"
title="">
<!-- Disable Folder icon
<img src="" height="16" width="16" alt=""
class="navIcon"
tal:condition="not:isAnon"
tal:attributes="src python:portal_url+'/'+sibling.getIcon(1);
title sibling/Type;" />
-->
<span class="navItemText">BioC2006</span>
</a>
<a href="../../../aucklandwksp/index.html"
accesskey="n"
class="navItem navLevel3"
title="">
<!-- Disable Folder icon
<img src="" height="16" width="16" alt=""
class="navIcon"
tal:condition="not:isAnon"
tal:attributes="src python:portal_url+'/'+sibling.getIcon(1);
title sibling/Type;" />
-->
<span class="navItemText">Workshops on S, R and Bioconductor</span>
</a>
<a href="../../../biocintro_april/index.html"
accesskey="n"
class="navItem navLevel3"
title="April Intro R/Bioc Course at FHCRC">
<!-- Disable Folder icon
<img src="" height="16" width="16" alt=""
class="navIcon"
tal:condition="not:isAnon"
tal:attributes="src python:portal_url+'/'+sibling.getIcon(1);
title sibling/Type;" />
-->
<span class="navItemText">R/Bioc Intro Course</span>
</a>
<a href="../../../rforbioinformatics/index.html"
accesskey="n"
class="navItem navLevel3"
title="Course materials. The course took place at FHCRC Seattle in January 2006">
<!-- Disable Folder icon
<img src="" height="16" width="16" alt=""
class="navIcon"
tal:condition="not:isAnon"
tal:attributes="src python:portal_url+'/'+sibling.getIcon(1);
title sibling/Type;" />
-->
<span class="navItemText">R for Bioinformatics</span>
</a>
<a href="../../../../2005/index.html"
accesskey="n"
class="navItem navLevel2"
title="">
<!-- Disable Folder icon
<img src="" height="16" width="16" alt=""
class="navIcon"
tal:condition="not:isAnon"
tal:attributes="src python:portal_url+'/'+sibling.getIcon(1);
title sibling/Type;" />
-->
<span class="navItemText">2005</span>
</a>
<a href="../../../../2004/index.html"
accesskey="n"
class="navItem navLevel2"
title="">
<!-- Disable Folder icon
<img src="" height="16" width="16" alt=""
class="navIcon"
tal:condition="not:isAnon"
tal:attributes="src python:portal_url+'/'+sibling.getIcon(1);
title sibling/Type;" />
-->
<span class="navItemText">2004</span>
</a>
<a href="../../../../2003/index.html"
accesskey="n"
class="navItem navLevel2"
title="">
<!-- Disable Folder icon
<img src="" height="16" width="16" alt=""
class="navIcon"
tal:condition="not:isAnon"
tal:attributes="src python:portal_url+'/'+sibling.getIcon(1);
title sibling/Type;" />
-->
<span class="navItemText">2003</span>
</a>
<a href="../../../../2002/index.html"
accesskey="n"
class="navItem navLevel2"
title="Workshops and courses 2002">
<!-- Disable Folder icon
<img src="" height="16" width="16" alt=""
class="navIcon"
tal:condition="not:isAnon"
tal:attributes="src python:portal_url+'/'+sibling.getIcon(1);
title sibling/Type;" />
-->
<span class="navItemText">2002</span>
</a>
<a href="../../../../../developers/index.html"
accesskey="n"
class="navItem navLevel1"
title="">
<!-- Disable Folder icon
<img src="" height="16" width="16" alt=""
class="navIcon"
tal:condition="not:isAnon"
tal:attributes="src python:portal_url+'/'+sibling.getIcon(1);
title sibling/Type;" />
-->
<span class="navItemText">Developers</span>
</a>
<a href="../../../../../News/index.html"
accesskey="n"
class="navItem navLevel1"
title="BioC Project News">
<!-- Disable Folder icon
<img src="" height="16" width="16" alt=""
class="navIcon"
tal:condition="not:isAnon"
tal:attributes="src python:portal_url+'/'+sibling.getIcon(1);
title sibling/Type;" />
-->
<span class="navItemText">News</span>
</a>
</div>
</div>
</div>
</div>
</div>
</div>
<!-- end of the left (by default at least) column -->
</div>
<!-- end of the main and left columns -->
<!-- start of right (by default at least) column -->
<div id="portal-column-two">
<div class="visualPadding">
<div>
<!-- The Related Items box -->
<script type="text/javascript" src="plonesearchbox_utils.js">
</script>
<div class="portlet">
<!--
<h5 i18n:translate="searchbox_title">Search Box</h5>
-->
<div class="portletBody">
<form name="searchbox_form" id="searchbox_form"
method="post" onsubmit="return process()"
action="http://bioconductor.org/workshops/2006/biocintro_oct/labs/Affy/redirectToUrl" target="_blank">
<div class="portletContent odd">
<div id="searchbox_fields">
<input type="text" name="toSearch" id="toSearch" size="22" />
</div>
<select name="choice" id="choice" onchange="return generateForm();" style="margin: 3px 0px 0px 0px;">
<option value="http://bioconductor.org/workshops/2006/biocintro_oct/labs/Affy/AffyLab-lab.R/search?SearchableText="
id="search_portal">In this site</option>
<option value="http://bioconductor.org/workshops/2006/biocintro_oct/labs/Affy/AffyLab-lab.R/search?path=/Plones/rgentlem/bioconductor/workshops/2006/biocintro_oct/labs/Affy/AffyLab-lab.R&SearchableText="
id="search_rubric">In this folder</option>
<option value="http://google.com/search?sitesearch=www.bioconductor.org&q=%(text)s">Google this site</option>
</select>
<input class="context searchButton" type="submit"
value="Search" style="margin: 3px;" />
</div>
<!--
<div class="portletContent odd">
<input class="context searchButton" type="submit" value="Search" style="margin: 3px;" i18n:attributes="value"/>
</div>
<div class="portletContent even">
<a href="" tal:attributes="href string:${portal_url}/search_form" i18n:translate="advanced_search_link">Advanced search</a>
</div>
-->
</form>
<script type="text/javascript">
<!--
/*in case the first choice of the combobox is an url with several fields*/
clearForm();
generateForm();
-->
</script>
</div>
</div>
</div>
<div class="portlet" id="portlet-news">
<h5>News</h5>
<div class="portletBody">
<div class="portletContent odd">
<div class="portletDetails">
<a href="../../../../../News/2009-10-28-Release-2.5"
class="date"
title="BioC 2.5 Released">2009-10-26</a>
<p>
BioC 2.5, consisting of 352 packages and designed to work with R 2.10.z, was released today.
</p>
</div>
</div>
<div class="portletContent even">
<div class="portletDetails">
<a href="../../../../../News/RinNYT"
class="date"
title="Print Media Recognition">2009-01-07</a>
<p>
R, the open source platform used by Bioconductor, featured in a series of articles in the New York Times.
</p>
</div>
</div>
<div class="portletContent odd">
<a href="../../../../../news"
class="portletMore">
More...
</a>
</div>
</div>
</div>
</div>
</div>
<!-- end of the right (by default at least) column -->
</div>
<!-- end column wrapper -->
<div class="visualClear"></div>
<hr class="netscape4" />
<div id="portal-footer">
© 2003-2009 BioConductor. All Rights Reserved.
<script type="text/javascript">
var gaJsHost = (("https:" == document.location.protocol) ? "https://ssl." : "http://www.");
document.write(unescape("%3Cscript src='" + gaJsHost + "google-analytics.com/ga.js' type='text/javascript'%3E%3C/script%3E"));
</script>
<script type="text/javascript">
try{
var pageTracker = _gat._getTracker("UA-357281-1");
pageTracker._trackPageview();
} catch(err) {}
</script>
</div>
</div>
</body>
</html>