Update help of duplicate filter
<h2>Description</h2>
<p>
-Two peaks are considered duplicates when their m/z and retention time differences are lower than
+Three different modes:<br>
+<b>Old average</b> (the old filter): Keeps only the feature list row with the maximum average area. Checks for average m/z and RT.<br>
+<b>New average</b>: Two peaks are considered duplicates when their average m/z and retention time differences are lower than
the tolerances set by the user. When two (or more) duplicates are found, a consensus row is created with the lowest row ID of all duplicates. For this consensus
row, all <span style="background-color: #00FF00"><b>DETECTED</b></span> features are favored over <span style="background-color: #FFFF00"><b>ESTIMATED</b></span> (gap-filled) and ESTIMATED are favored over <span style="background-color: #FF0000"><b>UNKNOWN</b></span>.
-Furthermore, if there are only <span style="background-color: #FFFF00"><b>ESTIMATED</b></span> features in a raw data file, the highest is chosen.
+Furthermore, if there are only <span style="background-color: #FFFF00"><b>ESTIMATED</b></span> features in a raw data file, the highest is chosen.<br>
+<b>Single feature</b>: Marks rows as duplicates if they share one feature within the RT and m/z tolerance in the same raw data file. Creates a consensus row.
</p>
<h4>Notes</h4>
@@ -29,9 +32,10 @@ To use this filter, turn off the average option.
<dt>Name sufix</dt>
<dd>This is the suffix to identify the new aligned peak list in Peak list frame of desktop.</dd>
-<dt>Filter average m/z and RT</dt>
-<dd>If checked: Compares rows with the average m/z and RT (like the old algorithm)</dd>
-<dd>If not: Compares rows on a raw data file basis. Marks rows as duplicates if two rows share a feature in a raw data file with the same RT and m/z (and identity/charge state)</dd>
+<dt>Filter mode:</dt>
+<dd>Old average: Compares rows with the average m/z and RT (like the old algorithm)</dd>
+<dd>New average: Compares rows with the average m/z and RT. Creates a consensus row</dd>
+<dd>Single feature: Compares rows on a raw data file basis. Marks rows as duplicates if two rows share a feature in a raw data file with the same RT and m/z (and identity/charge state)</dd>
<dt>M/Z tolerance</dt>
<dd>Maximum m/z difference between duplicate peaks.</dd>
@@ -49,7 +53,7 @@ To use this filter, turn off the average option.
<p>
- <h4>Aligned, gap-filled feature list prior and after duplicate row filter.</h4>
+ <h4>Aligned, gap-filled feature list prior and after duplicate row filter (new average).</h4>
<img src="prior.png" name="prior">
<img src="after.png" name="after">
</p>
