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<head><title>Quick Start guide &lt; Help &lt; ArrayExpress &lt; EMBL-EBI</title></head>
<body class="level2">
    <div id="content" role="main" class="grid_24 clearfix">
        <section id="ae-help" class="grid_18 alpha">
            <h2>Quick Start guide</h2>
            <ol>
                <li><a href="#SearchResultsTable">Experiments table</a></li>
                <li><a href="#SingleExptView">Single experiment overview</a></li>
                <li><a href="#SamplesTable">Samples table</a></li>
                <li><a href="#FilesForDownload">Files for download</a></li>
                <li><a href="#BamFilesEnsembl">BAM files for RNA-seq experiments</a></li>
                <li><a href="#MoreHelp">More help</a></li>
            </ol>
            <br>
            <p><span class='icon icon-generic' data-icon='l'></span><i>Under each topic, click on the screenshot or <span class='icon icon-generic' data-icon='?'></span>help link to get bite-size guide in EBI Train Online tutorials (will open in a new browser window or tab).</i></p>
            <p>&nbsp;</p>
            <h3><a id="SearchResultsTable">1. Experiments table</a></h3>
            <p>This is the table of experiments you'll see when you go to the ArrayExpress <a href="/arrayexpress/experiments/browse.html">Experiments</a> tab, one row per experiment. The experiments displayed depend on search terms you've entered or filters you've selected.</p>
            <p><a href="/training/online/course/arrayexpress-exploring-functional-genomics-data-ar/how-search-archive" target="_blank" class='icon icon-generic' data-icon='?'><strong>Tour the experiments table in section 2 of Train Online tutorial "How to search ArrayExpress"</strong><img src="understand_search_results_table.png" alt="Search results table"></a></p>
            <p style="text-align: right;"><a href="#top" class="linktotop">Top</a></p>
            <h3><a id="SingleExptView">2. Single experiment overview</a></h3>
            <p>When you click on an experiment on the <a href="#SearchResultsTable">Experiments table</a>, e.g. <a href="/arrayexpress/experiments/E-MTAB-777">"http://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-777"</a>, you will come to this page which summarises all the information and data download links for an experiment. There are also links to <a href="www.genomespace.org">GenomeSpace</a> and R ExpressionSet objects.</p>
            <p><a href="/training/online/course/arrayexpress-exploring-functional-genomics-data-ar/how-search-archive" target="_blank" class='icon icon-generic' data-icon='?'><strong>Discover features of this overview in section 5 of Train Online tutorial "How to search ArrayExpress"</strong><img src="understand_single_expt_overview.png" alt="Single experiment view"></a></p>
            <p style="text-align: right;"><a href="#top" class="linktotop">Top</a></p>
            <h3><a id="SamplesTable">3. Samples table</a></h3>
            <p>You'll get to this table from the link <i>"Click for detailed sample information and links to data"</i> on the <a href="#SingleExptView">Single experiment overview page</a>, e.g. <a href="/arrayexpress/experiments/E-MTAB-674/samples.html">http://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-674/samples.html</a>. Here, samples are in rows and sample attributes are in columns. You'll also find direct link to data files for each sample in the last column.</p>
            <p>To download the full samples table, just use the link at the bottom of the table. The downloaded file is tab-delimited text file, which can be opened in any spreadsheet programme.</p>
            <p><a href="/training/online/course/arrayexpress-exploring-functional-genomics-data-ar/how-search-archive" target="_blank" class='icon icon-generic' data-icon='?'><strong>See annotated samples table in section 6 of Train Online tutorial "How to search ArrayExpress"</strong><img src="understand_samples_view.png" alt="Experiment samples view"></a></p>
            <p style="text-align: right;"><a href="#top" class="linktotop">Top</a></p>
            <h3><a id="FilesForDownload">4. Files for download</a></h3>
            <p>On the <a href="#SingleExptView">Single experiment overview page</a>, you can download all files (e.g. sample annotations, raw data files) for the experiment using links in the <i>"Files"</i> section, e.g. <a href="/arrayexpress/experiments/E-MTAB-674/files/">http://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-674/files/"</a>.</p>
            <p><a href="/training/online/course/arrayexpress-exploring-functional-genomics-data-ar/how-get-data-archive" target="_blank" class='icon icon-generic' data-icon='?'><strong>Find out more about data files in Train Online tutorial "How to get data from ArrayExpress"</strong><img src="understand_experiment_files.png" alt="Experiment files view"></a></p>
            <p style="text-align: right;"><a href="#top" class="linktotop">Top</a></p>
            <h3><a id="BamFilesEnsembl">5. BAM files for RNA-seq experiments</a></h3>
            <p>For a subset of highly-curated RNA-seq experiments in ArrayExpress, e.g. <a href="/arrayexpress/experiments/E-MTAB-513/samples/">http://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-513/samples/</a>, we created BAM files by processing the experimental raw FASTQ data files with the <a href="http://bioconductor.org/packages/release/bioc/html/ArrayExpressHTS.html">ArrayExpressHTS BioConductor package</a> as part of the <a href="http://europepmc.org/abstract/MED/21233166">RNA-seq data processing pipeline</a>. The BAM files are available for download and can also be viewed in <a href="http://www.ensembl.org">Ensembl</a>.</p>
            <p><a href="/training/online/course/arrayexpress-exploring-functional-genomics-data-ar/when-use-archive-some-examples/high-throug" target="_blank" class='icon icon-generic' data-icon='?'><strong>Find out about the BAM files in Train Online tutorial "High-throughput sequencing" sections 3-4</strong><img src="understand_ensembl_link.png" alt="BAM files in Ensembl Genome Browser"></a></p>
            <p style="text-align: right;"><a href="#top" class="linktotop">Top</a></p>
            <h3><a id="MoreHelp">6. More help</a></h3>
            <p>For a comprehensive guide on using ArrayExpress, please try our free, online tutorial:<br><br>
                <a href="/training/online/course/arrayexpress-exploring-functional-genomics-data-ar/" target="_blank" class='icon icon-generic' data-icon='t'>Train Online tutorial - ArrayExpress: Exploring functional genomics data with the ArrayExpress</a></p>
            <p>If you are submitting data to us for the first time, you will find guidelines and tips in:<br><br>
                <a href="/training/online/course/arrayexpress-submitting-data-using-mage-tab" target="_blank" class='icon icon-generic' data-icon='t'>Train Online tutorial - ArrayExpress: Submitting data using MAGE-TAB</a><br><commit_msg>Updated section on ArrayExpress-generated BAM files.<commit_after><!DOCTYPE html>
<html class="no-js" lang="en">
<head><title>Quick Start guide &lt; Help &lt; ArrayExpress &lt; EMBL-EBI</title></head>
<body class="level2">
    <div id="content" role="main" class="grid_24 clearfix">
        <section id="ae-help" class="grid_18 alpha">
            <h2>Quick Start guide</h2>
            <ol>
                <li><a href="#SearchResultsTable">Experiments table</a></li>
                <li><a href="#SingleExptView">Single experiment overview</a></li>
                <li><a href="#SamplesTable">Samples table</a></li>
                <li><a href="#FilesForDownload">Files for download</a></li>
                <li><a href="#BamFilesEnsembl">BAM files for RNA-seq experiments</a></li>
                <li><a href="#MoreHelp">More help</a></li>
            </ol>
            <br>
            <p><span class='icon icon-generic' data-icon='l'></span><i>Under each topic, click on the screenshot or <span class='icon icon-generic' data-icon='?'></span>help link to get bite-size guide in EBI Train Online tutorials (will open in a new browser window or tab).</i></p>
            <p>&nbsp;</p>
            <h3><a id="SearchResultsTable">1. Experiments table</a></h3>
            <p>This is the table of experiments you'll see when you go to the ArrayExpress <a href="/arrayexpress/experiments/browse.html">Experiments</a> tab, one row per experiment. The experiments displayed depend on search terms you've entered or filters you've selected.</p>
            <p><a href="/training/online/course/arrayexpress-exploring-functional-genomics-data-ar/how-search-archive" target="_blank" class='icon icon-generic' data-icon='?'><strong>Tour the experiments table in section 2 of Train Online tutorial "How to search ArrayExpress"</strong><img src="understand_search_results_table.png" alt="Search results table"></a></p>
            <p style="text-align: right;"><a href="#top" class="linktotop">Top</a></p>
            <h3><a id="SingleExptView">2. Single experiment overview</a></h3>
            <p>When you click on an experiment on the <a href="#SearchResultsTable">Experiments table</a>, e.g. <a href="/arrayexpress/experiments/E-MTAB-777">"http://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-777"</a>, you will come to this page which summarises all the information and data download links for an experiment. There are also links to <a href="www.genomespace.org">GenomeSpace</a> and R ExpressionSet objects.</p>
            <p><a href="/training/online/course/arrayexpress-exploring-functional-genomics-data-ar/how-search-archive" target="_blank" class='icon icon-generic' data-icon='?'><strong>Discover features of this overview in section 5 of Train Online tutorial "How to search ArrayExpress"</strong><img src="understand_single_expt_overview.png" alt="Single experiment view"></a></p>
            <p style="text-align: right;"><a href="#top" class="linktotop">Top</a></p>
            <h3><a id="SamplesTable">3. Samples table</a></h3>
            <p>You'll get to this table from the link <i>"Click for detailed sample information and links to data"</i> on the <a href="#SingleExptView">Single experiment overview page</a>, e.g. <a href="/arrayexpress/experiments/E-MTAB-674/samples.html">http://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-674/samples.html</a>. Here, samples are in rows and sample attributes are in columns. You'll also find direct link to data files for each sample in the last column.</p>
            <p>To download the full samples table, just use the link at the bottom of the table. The downloaded file is tab-delimited text file, which can be opened in any spreadsheet programme.</p>
            <p><a href="/training/online/course/arrayexpress-exploring-functional-genomics-data-ar/how-search-archive" target="_blank" class='icon icon-generic' data-icon='?'><strong>See annotated samples table in section 6 of Train Online tutorial "How to search ArrayExpress"</strong><img src="understand_samples_view.png" alt="Experiment samples view"></a></p>
            <p style="text-align: right;"><a href="#top" class="linktotop">Top</a></p>
            <h3><a id="FilesForDownload">4. Files for download</a></h3>
            <p>On the <a href="#SingleExptView">Single experiment overview page</a>, you can download all files (e.g. sample annotations, raw data files) for the experiment using links in the <i>"Files"</i> section, e.g. <a href="/arrayexpress/experiments/E-MTAB-674/files/">http://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-674/files/"</a>.</p>
            <p><a href="/training/online/course/arrayexpress-exploring-functional-genomics-data-ar/how-get-data-archive" target="_blank" class='icon icon-generic' data-icon='?'><strong>Find out more about data files in Train Online tutorial "How to get data from ArrayExpress"</strong><img src="understand_experiment_files.png" alt="Experiment files view"></a></p>
            <p style="text-align: right;"><a href="#top" class="linktotop">Top</a></p>
            <h3><a id="BamFilesEnsembl">5. BAM files for RNA-seq experiments</a></h3>
            <p>For a subset of RNA-seq experiments in ArrayExpress, e.g. <a href="/arrayexpress/experiments/E-MTAB-822/samples/">https://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-822/samples/</a>, we created BAM files by processing the experimental raw FASTQ data files with the <a href="http://bioconductor.org/packages/release/bioc/html/ArrayExpressHTS.html">ArrayExpressHTS BioConductor package</a> as part of the <a href="http://europepmc.org/abstract/MED/21233166">RNA-seq data processing pipeline</a>. The BAM files are <a href="arrayexpress/experiments/E-MTAB-822/files">available for download</a> and can also be viewed in <a href="http://www.ensembl.org">Ensembl</a>.</p>
            <p><a href="/training/online/course/arrayexpress-exploring-functional-genomics-data-ar/when-use-archive-some-examples/high-throug" target="_blank" class='icon icon-generic' data-icon='?'><strong>Find out about the BAM files in Train Online tutorial "High-throughput sequencing" sections 3-4</strong><img src="understand_ensembl_link.png" alt="BAM files in Ensembl Genome Browser"></a></p>
            <p style="text-align: right;"><a href="#top" class="linktotop">Top</a></p>
            <h3><a id="MoreHelp">6. More help</a></h3>
            <p>For a comprehensive guide on using ArrayExpress, please try our free, online tutorial:<br><br>
                <a href="/training/online/course/arrayexpress-exploring-functional-genomics-data-ar/" target="_blank" class='icon icon-generic' data-icon='t'>Train Online tutorial - ArrayExpress: Exploring functional genomics data with the ArrayExpress</a></p>
            <p>If you are submitting data to us for the first time, you will find guidelines and tips in:<br><br>
                <a href="/training/online/course/arrayexpress-submitting-data-using-mage-tab" target="_blank" class='icon icon-generic' data-icon='t'>Train Online tutorial - ArrayExpress: Submitting data using MAGE-TAB</a><br>
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