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<article role="main" id="furo-main-content">
<section id="dna-methylation-array-data-standard-v-2410">
<h1>DNA Methylation Array Data Standard V-2410<a class="headerlink" href="#dna-methylation-array-data-standard-v-2410" title="Link to this heading">¶</a></h1>
<p>This standard describes a consistent file format for methylation matrix data and associated metadata.
It focuses on file formatting for storage and transmission without mandating any specific form of data processing.</p>
<section id="why-is-this-standard-needed">
<h2>Why is this standard needed?<a class="headerlink" href="#why-is-this-standard-needed" title="Link to this heading">¶</a></h2>
<p>GEO Series Matrix files are a very commonly used standard for representing methylation data and sample metadata. However, they have two problems:</p>
<ul class="simple">
<li><p>While metadata field inclusion follows a standard format, GEO does not standardize metadata values even for common data fields like sex and age.</p></li>
<li><p>As methylation data has grown larger, the matrix can no longer be included in the Series Matrix files and is instead added as a supplementary file; however, these files do not have a standard format.</p></li>
</ul>
</section>
<section id="preprocessing">
<h2>Preprocessing<a class="headerlink" href="#preprocessing" title="Link to this heading">¶</a></h2>
<p>This standard assumes that the array data has been pre-processed, including quality control, batch correction, and normalization.
We recommend using SeSAMe for preprocessing, as recommended by Illumina.</p>
</section>
<section id="methylation-matrix-file-standard">
<h2>Methylation Matrix File Standard<a class="headerlink" href="#methylation-matrix-file-standard" title="Link to this heading">¶</a></h2>
<section id="file-format">
<h3>File Format<a class="headerlink" href="#file-format" title="Link to this heading">¶</a></h3>
<ul class="simple">
<li><p>Files must be formatted as CSV (Comma-Separated Values).</p></li>
<li><p>Each row in the file must contain the same number of entries.</p></li>
<li><p><strong>Rows</strong>: Each row corresponds to measurements for a CpG site, with the CpG ID in the first column.</p></li>
<li><dl class="simple">
<dt><strong>Columns</strong>: Each column corresponds to a sample, with the sample ID as the header.</dt><dd><ul>
<li><p><strong>Header Row</strong>: The first row must contain sample IDs.</p></li>
<li><p>If published on GEO, the sample IDs must match GEO IDs exactly.</p></li>
</ul>
</dd>
</dl>
</li>
<li><p><strong>Length</strong>: No more than 1000 samples should be included in a single file.</p></li>
</ul>
</section>
<section id="data-values">
<h3>Data Values<a class="headerlink" href="#data-values" title="Link to this heading">¶</a></h3>
<ul class="simple">
<li><p><strong>Beta Values</strong>: All data values must be beta values (methylation levels).</p></li>
<li><p><strong>Range</strong>: Beta values must be decimal numbers between 0 and 1 or “NaN”.</p></li>
<li><p><strong>Precision</strong>: Beta values must be rounded to no more than three decimal places.</p></li>
<li><p><strong>Handling Multiple Values</strong>: If multiple values exist for the same CpG site, use the average of the available values.</p></li>
</ul>
</section>
</section>
<section id="metadata-file-standard">
<h2>Metadata File Standard<a class="headerlink" href="#metadata-file-standard" title="Link to this heading">¶</a></h2>
<section id="id1">
<h3>File Format<a class="headerlink" href="#id1" title="Link to this heading">¶</a></h3>
<ul class="simple">
<li><p>Files must be formatted as CSV (Comma-Separated Values).</p></li>
<li><p>Each row represents a sample, and each column represents a metadata field.</p></li>
</ul>
</section>
<section id="standard-metadata-fields">
<h3>Standard Metadata Fields<a class="headerlink" href="#standard-metadata-fields" title="Link to this heading">¶</a></h3>
<ul class="simple">
<li><p><strong>Sex</strong>: Integer value with 0 for female and 1 for male. “NaN” (no values) is permitted for unknown values.</p></li>
<li><p><strong>Age</strong>: Integer or decimal value representing age in years.</p></li>
</ul>
</section>
<section id="additional-metadata-fields">
<h3>Additional Metadata Fields<a class="headerlink" href="#additional-metadata-fields" title="Link to this heading">¶</a></h3>
<ul class="simple">
<li><p>Other metadata fields are permitted.</p></li>
</ul>
</section>
</section>
<section id="example-files">
<h2>Example Files<a class="headerlink" href="#example-files" title="Link to this heading">¶</a></h2>
<p>Example DNAm File:</p>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">cpgSite</span> <span class="n">GSM3074480</span> <span class="n">GSM3074481</span> <span class="n">GSM3074482</span> <span class="n">GSM3074483</span>
<span class="n">cg00000029</span> <span class="mf">0.395</span> <span class="mf">0.499</span> <span class="mf">0.42</span> <span class="mf">0.423</span>
<span class="n">cg00000109</span> <span class="mf">0.821</span> <span class="mf">0.868</span> <span class="mf">0.877</span> <span class="mf">0.841</span>
<span class="n">cg00000155</span> <span class="mf">0.878</span> <span class="mf">0.89</span> <span class="mf">0.894</span> <span class="mf">0.822</span>
</pre></div>
</div>
<p>Example Metadata File:</p>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">SampleID</span> <span class="n">Sex</span> <span class="n">Age</span> <span class="n">Disease</span> <span class="n">State</span>
<span class="n">GSM3074480</span> <span class="mi">0</span> <span class="mf">25.2</span> <span class="kc">None</span>
<span class="n">GSM3074481</span> <span class="mi">0</span> <span class="mf">29.5</span> <span class="n">COVID</span>
<span class="n">GSM3074482</span> <span class="mi">1</span> <span class="mf">39.7</span> <span class="kc">None</span>
</pre></div>
</div>
</section>
<section id="references">
<h2>References<a class="headerlink" href="#references" title="Link to this heading">¶</a></h2>
<ul class="simple">
<li><p><a class="reference external" href="https://www.encodeproject.org/data-standards/">Data standards – ENCODE</a></p></li>
<li><p><a class="reference external" href="https://www.ncbi.nlm.nih.gov/geo/info/soft.html">SOFT file format and content - GEO - NCBI</a></p></li>
<li><p><a class="reference external" href="https://www.illumina.com/techniques/microarrays/methylation-arrays/methylation-array-data-analysis-tips.html">Methylation Array Data Analysis Tips - Illumina</a></p></li>
</ul>
</section>
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<ul>
<li><a class="reference internal" href="#">DNA Methylation Array Data Standard V-2410</a><ul>
<li><a class="reference internal" href="#why-is-this-standard-needed">Why is this standard needed?</a></li>
<li><a class="reference internal" href="#preprocessing">Preprocessing</a></li>
<li><a class="reference internal" href="#methylation-matrix-file-standard">Methylation Matrix File Standard</a><ul>
<li><a class="reference internal" href="#file-format">File Format</a></li>
<li><a class="reference internal" href="#data-values">Data Values</a></li>
</ul>
</li>
<li><a class="reference internal" href="#metadata-file-standard">Metadata File Standard</a><ul>
<li><a class="reference internal" href="#id1">File Format</a></li>
<li><a class="reference internal" href="#standard-metadata-fields">Standard Metadata Fields</a></li>
<li><a class="reference internal" href="#additional-metadata-fields">Additional Metadata Fields</a></li>
</ul>
</li>
<li><a class="reference internal" href="#example-files">Example Files</a></li>
<li><a class="reference internal" href="#references">References</a></li>
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