Analysis of Gene Expression Data Short Course, JSM2005

<body> <center> <a href="http://www.amstat.org/meetings/jsm/2005/" target="_TOP"><img src="images/index_01crop.gif" alt="index_01crop.gif" border=0></a> <img src="images/index_02crop.gif" alt="index_02crop.gif" border=0> </center> <center> <a href="http://www.amstat.org/meetings/jsm/2005/" target="_TOP"><img src="images/index_456.jpg" alt="index_456.jpg" border=0></a> </center> <table width=614 align=center STYLE="background-image: url('images/index_16.gif'); border: 0 ridge #800000"><tr> <td colspan=4 height="2"><img src="images/spacer.gif" alt="spacer.gif" width="100%" height="2"></td> </tr></table> <h3 align="center"><i><br> Using Our Discipline to Enhance Human Welfare<br> August 7 - 11, 2005</i></h3> <H1>Analysis of Gene Expression Data Short Course, JSM2005</H1> <P align=center>Terry Speed<SUP>1,2</SUP>, Jean Yang<SUP>3</SUP>, Ben Bolstad<SUP>2</SUP> and James Wettenhall<SUP>1</SUP> <BR>Augst 6-7, 2005</P> <P align=center> 1. Walter and Eliza Hall Institute of Medical Research<BR> 2. Department of Statistics, University of California, Berkeley<br> 3. University of Sydney</P> <H2>Course Outline</H2> <UL> <LI><A href="http://bioinf.wehi.edu.au/marray/jsm2005/outline.pdf">outline.pdf</A> </LI></UL> <H2>Lecture Slides in PDF format (Annotation slides added Aug 22)</H2> <UL> <LI><A href="http://bioinf.wehi.edu.au/marray/jsm2005/lectures/lectPDF.html">http://bioinf.wehi.edu.au/marray/jsm2005/lectures/lectPDF.html</A></LI></UL> <H2>Lab Exercises</H2> <P>Each lab description lists the required software and data for that lab. An overall list of software for the entire workshop is given in the following section (Required Software).</P>  <OL> <LI><B>Lab 1.</B> <A href="http://bioinf.wehi.edu.au/marray/jsm2005/lab1/lab1.html">lab1.html</A> <A href="http://bioinf.wehi.edu.au/marray/jsm2005/lab1/lab1.pdf">lab1.pdf</A> <UL> <LI><I>Reading raw two-color microarray data into R, comparing the performance of different image analysis software using diagnostic plots, identifying control spots and blank spots on the arrays, and normalizing the data.</I> </LI></UL> <LI><B>Lab 2.</B> <A href="http://bioinf.wehi.edu.au/marray/jsm2005/lab2/lab2.html">lab2.html</A> <A href="http://bioinf.wehi.edu.au/marray/jsm2005/lab2/lab2.pdf">lab2.pdf</A> <UL> <LI><I>A continuation of the topics from lab 1, using a different data set.</I> </LI></UL> <LI><B>Lab 3.</B> <A href="http://bioinf.wehi.edu.au/marray/jsm2005/lab3/lab3.html">lab3.html</A> <A href="http://bioinf.wehi.edu.au/marray/jsm2005/lab3/lab3.pdf">lab3.pdf</A> <UL> <LI><I>Reading raw Affymetrix microarray data into R, assessing the quality of the data using diagnostic plots, and normalizing the data.</I> </LI></UL> <LI><B>Lab 4.</B> <A href="http://bioinf.wehi.edu.au/marray/jsm2005/lab4/lab4.html">lab4.html</A> <A href="http://bioinf.wehi.edu.au/marray/jsm2005/lab4/lab4.pdf">lab4.pdf</A> <UL> <LI><I>Fitting linear models to microarray data, finding differentially expressed genes, linking gene lists to external databases, using diagnostic plots to assess the performance of the linear model, and using Venn diagrams to find genes differentially expressed for more than one pair of conditions. </I></LI></UL> <LI><B>Lab 5.</B> <A href="http://bioinf.wehi.edu.au/marray/jsm2005/lab5/lab5.html">lab5.html</A> <A href="http://bioinf.wehi.edu.au/marray/jsm2005/lab5/lab5.pdf">lab5.pdf</A> <UL> <LI><I>Advanced Linear Modelling and Time-Series Analysis</I> </LI></UL></LI> <LI><B>Lab 6.</B> <A href="http://bioinf.wehi.edu.au/marray/jsm2005/lab6/lab6.html">lab6.html</A> <A href="http://bioinf.wehi.edu.au/marray/jsm2005/lab6/JSMLab6.RData">JSMLab6.RData</A> <A href="http://bioinf.wehi.edu.au/marray/jsm2005/lab6/Lab6Rcode.R">Lab6Rcode.R</A> <UL> <LI><I>Classification and clustering of microarray data.</I> </LI></UL></LI> <LI><B>Lab 7.</B> <A href="http://bioinf.wehi.edu.au/marray/jsm2005/lab7/lab7.html">lab7.html</A> <A href="http://bioinf.wehi.edu.au/marray/jsm2005/lab7/lab7.pdf">lab7.pdf</A> <UL> <LI><I>Gene ontologies and gene sets. Finding statistically significant over-represented (or under-represented) gene ontologies in a set of differentially expressed genes compared to a reference list of genes. Methods for determining whether a pre-defined set of genes is differentially expressed in circumstances where it is difficult to measure whether individual genes are differentially expressed. </I></LI></UL> </OL> <H2>Required Software</H2> <UL> <LI><A href="http://bioinf.wehi.edu.au/marray/jsm2005/Required/" target="_TOP">http://bioinf.wehi.edu.au/marray/jsm2005/Required/</A> </LI></UL> <P>As well as checking the overall list of required software, you may also wish to check each individual lab sheet for a list of software required for that lab.</P> <H2>Required Data</H2> <P>Please check whether you already have the "Drosophila Embryo", "Hyperdip" and "Estrogen" packages from the Required Software. (These data sets are stored within R packages.)</P> <UL> <LI><A href="http://bioinf.wehi.edu.au/marray/jsm2005/Data/swirl.zip">Swirl Zebrafish Data</A> (2.4 MB)</LI> <LI><A href="http://bioinf.wehi.edu.au/marray/jsm2005/Data/CellLine.zip">Cell line comparison Data</A> (12.1 MB)</LI> <LI><A href="http://bioinf.wehi.edu.au/marray/jsm2005/Data/CellLineImages.zip">Array images for cell line comparison Data</A> (1.8 MB)</LI> <LI><b>Drosophila Embryo Data (as an R package)</b> <a href="Required/Software/drosEmbryo_1.0.zip">Windows</A>    <a href="Required/Software/drosEmbryo_1.0.tar.gz">Source (Mac,Linux)</a> (3.5 MB)</LI> <LI><b>Hyperdip Data (as an R package)</b> <a href="Required/Software/jsmHyperdip_1.0.zip">Windows</A>    <a href="Required/Software/jsmHyperdip_1.0.tar.gz">Source (Mac,Linux)</a> (5 MB)</LI> <LI><b>Estrogen Data (as an R package)</b> <a href="http://www.bioconductor.org/packages/data/experiment/stable/src/contrib/Win32/estrogen_1.5.0.zip">Windows</A>    <a href="http://www.bioconductor.org/packages/data/experiment/stable/src/contrib/Source/estrogen_1.5.0.tar.gz">Source (Mac,Linux)</a> (36.3 MB)</LI> <LI><A href="http://bioinf.wehi.edu.au/marray/jsm2005/Data/EstrogenTargets.txt">EstrogenTargets.txt</A></LI> <li><A href="http://bioinf.wehi.edu.au/marray/jsm2005/lab6/JSMLab6.RData">JSMLab6.RData</A> (3.5 MB)</li> <LI><A href="http://bioinf.wehi.edu.au/marray/jsm2005/Data/apoai.zip">ApoAI Knockout Data</A> (1.2 MB)</LI> <LI><A href="http://bioinf.wehi.edu.au/marray/jsm2005/Data/knownERgenes.txt">knownERgenes Data</A> (1 KB)</LI> <LI><A href="http://bioinf.wehi.edu.au/marray/jsm2005/Data/predictedERgenes.txt">predictedERgenes Data</A> (38 KB)</LI> </UL> <H2>Past Microarary Workshops</H2> <UL> <LI><A href="http://www.ims.nus.edu.sg/Programs/microarray/tutorial.htm">Singapore Statistical Methods in Microarrays - IMS</A></LI> <LI><A href="http://www.bioconductor.org/workshops/Vienna03">DSC 2003 Bioconductor Workshop</A> (provides an introduction to genome biology)</LI> <LI><A href="http://www.bioconductor.org/workshop.html">Bioconductor short courses list</A> </LI></UL> <P><A href="http://validator.w3.org/check?uri=referer"><IMG height=31 alt="Valid HTML 4.0!" src="images/valid-html40.png" width=88 border=0></A> </P> <CENTER> <HR> <BR> <P>Comments/Questions? Contact <A href="mailto:wettenhall@wehi.edu.au">wettenhall@wehi.edu.au</A>. <EM><BR>Last modified: August 22, 2005 </EM></P></CENTER><BR><BR><BR><BR> </BODY>