https://sourceforge.net/p/altanalyze/wiki/QualityControl/Recent changes to QualityControlenSat, 01 Feb 2014 01:06:30 -0000https://sourceforge.net/p/altanalyze/wiki/QualityControl/<div class="markdown_content"><h2 id="quality-control-analyses-in-altanalyze">Quality Control Analyses in <a class="" href="/p/altanalyze/wiki/AltAnalyze/">AltAnalyze</a></h2> <p>Several quality control metrics are applied in <a class="" href="/p/altanalyze/wiki/AltAnalyze/">AltAnalyze</a> to identify putative outlier samples. The main output of all of these analyses are PDF and PNG image files output to the results directory under the folder <strong><code>DataPlots</code></strong>. A detailed description of these methods is provided <a class="" href="http://www.altanalyze.org/help.htm#QC" rel="nofollow">here</a>. </p> <h3 id="affymetrix">Affymetrix</h3> <ol> <li>Distribution of normalized log2 probeset intensity values </li> <li>Mean raw signal intensities of each array </li> <li>Mean absolute deviation (MAD) of the RMA residuals for each array </li> </ol> <h3 id="rna-seq">RNA-Seq</h3> <ol> <li>Distribution of log2 read-counts (exon and junction) </li> <li>Feature-level box-plots for the distribution of exon, junction and intron read-counts </li> <li>Total number of reads for each sample, broken down by exon, junction and intron aligning </li> </ol> <h3 id="all-platforms">All Platforms</h3> <ol> <li><a class="" href="/p/altanalyze/wiki/Heatmaps/">Hierarchical clustering</a> of significant genes and outliers </li> <li>Principal Component Analysis of samples (significant genes) </li> <li>Cell/tissue characterization of each sample (<a class="" href="/p/altanalyze/wiki/LineageProfiler/">LineageProfiler</a>) </li> </ol></div>AnonymousSat, 01 Feb 2014 01:06:30 -0000https://sourceforge.net8a64155100fa616606c4a6e8f0241e3c34cfa179