help_file_page.html

<h1 style="color: #5e9ca0;">User Manual</h1>
<h2>Data input</h2>
<p>Three types of files need to be uploaded.</p>
<ul>
<li>Raw data file: Single or multiple files can be uploaded either taken directly from the output file from the confocal (the first template) or data can be manually inputted into the second template file. Any columns in which no data is present should have 0 for each row.&nbsp;</li>
<li>The plate layout file: One file that defines the plate layout of treatments used. Numbers are defined by the treatment file.</li>
<li>The Treatment file: One file that defines the treatments. Multiple drugs and subsequent concentrations can be used.</li>
</ul>
<p><span style="color: #ff0000;">Note</span>: please download templates for these files and check that the column names of your files match the template's column names and sheet name matches the template's sheet name.</p>
<p>Previewing files in the main panel:</p>
<ul>
<li>Raw files can be previewed. A selection box is used for selecting different raw files if there are multiple raw files.</li>
<li>Treatment and layout can be viewed after both treatment and layout files have been uploaded. Users can view the plot of cells vs the selected value.</li>
</ul>
<h2>Outlier removal</h2>
<p>Choose the focal raw file in the selection panel for the outlier removal process.</p>
<p>Users can set Robust Z-score<sup>[1]</sup> and screen using pre-screen thresholds if required.</p>
<p>After clicking the Remove outliers button, outliers will be removed and plots will be displayed on the main panel. Plots can be viewed with the selected measurement (e.g. diameter, area, etc.).</p>
<p>Users can manually override cell results by selecting cells. The result of a selected cell will be toggled after applying the manual override (e.g. an outlier cell will be converted to a non-outlier cell).</p>
<p>The report of the selected file can be downloaded by clicking the download button.</p>
<h2>Merging</h2>
<p>A table of raw files will be shown on the main panel after uploading raw data files. The second column (column name: Processed) shows whether the file has gone through the outlier removal. The rest of the columns show the configuration (e.g. robust z score value) used in outlier removal. Downloaded outlier removal reports can also be uploaded and used in merging.</p>
<p>The merged file is only available when selected raw files have been processed.</p>
<h2>Plotting</h2>
<p>Plots of the merged data can be created and viewed. The app supports bar plots, point plots, dot plots and box plots.</p>
<p>Plots can be added to the report of files and downloaded.</p>
<p>&nbsp;</p>
<h2>References&nbsp;</h2>
<p>[1] Malo, N., Hanley, J., Cerquozzi, S., Pelletier, J. and Nadon, R., 2006. Statistical practice in high-throughput screening data analysis. <em>Nature Biotechnology</em>, 24(2), pp.167-175.</p>