https://sourceforge.net/p/altanalyze/wiki/ExpressionInput/Recent changes to ExpressionInputenSat, 01 Feb 2014 01:06:48 -0000https://sourceforge.net/p/altanalyze/wiki/ExpressionInput/<div class="markdown_content"><p>The <a class="" href="/p/altanalyze/wiki/ExpressionInput/">ExpressionInput</a> directory contains files used for all downstream <a class="" href="/p/altanalyze/wiki/AltAnalyze/">AltAnalyze</a> expression analyses. </p> <p>When beginning with Affymetrix CEL files, normalized expression values for all probesets are stored to this directory (exp.<a class="" href="../YourExperiment">YourExperiment</a>.txt) that result from APT (<a class="" href="/p/altanalyze/wiki/RMA/">RMA</a>). </p> <p>For splicing-sensitive arrays, a file containing detection probability statistics (<a class="" href="../DABG">DABG</a>) for all probesets is also saved (stats.<a class="" href="../YourExperiment">YourExperiment</a>.txt). </p> <p>When groups and comparisons are designated for your experimental samples, the files groups.<a class="" href="../YourExperiment">YourExperiment</a>.txt and comps.<a class="" href="../YourExperiment">YourExperiment</a>.txt are also saved here. </p> <p>In addition to these files, interim files created by <a class="" href="/p/altanalyze/wiki/AltAnalyze/">AltAnalyze</a> are also saved here and used by the program. Currently, these include probeset residuals (residuals.<a class="" href="../YourExperiment">YourExperiment</a>.txt) and constitutive gene summarized expression values (exp.<a class="" href="../YourExperiment">YourExperiment</a>-steady-state.txt). For RNASeq analyses, a file containing all original non-incremented read counts (counts.<a class="" href="../YourExperiment">YourExperiment</a>.txt) and gene-level total counts (counts.<a class="" href="../YourExperiment">YourExperiment</a>-steady-state.txt) will also be present. </p></div>AnonymousSat, 01 Feb 2014 01:06:48 -0000https://sourceforge.net73c9da8b43989c709db03ac2710f45f15e421b20