Changeset 3519

Timestamp:

Oct 1, 2015, 2:51:01 PM (8 years ago)

Author:

olle

Message:

Refs #801. Refs #815. Wizard "Create new start DNA plate" updated regarding dilution calculation and reporting:
a. The aliquot volume is increased from 10 to 10.5µl, i.e. volume of FPA + FPB from 20 to 21µl.
b. The dilution factor is now calculated from the ΔCt value using a function obtained by fitting an exponential curve to the Illumina step ladder dilution chart, instead of using the latter chart itself. The aim is to avoid large differences in dilution for extracts with ΔCt values on separate sides of a ladder step.
c. Dilution volumes for DNA and water, as well as ΔCt values, are now reported with 2 decimals instead of 1, in order to simplify checking the dilution calculation.

1. Javascript file select_dna_for_start_plate.js in resources/libprep/ updated:
   a. function getWellText(well)updated by increasing the aliquot volume from 10 to 10.5µl, and report dilution volumes for DNA and water, as well as ΔCt values, with 2 decimals instead of 1.
   b. Function fetchDilutionFactor(deltaCt) updated to calculate the dilution factor from the ΔCt value using a function obtained by fitting an exponential curve to the Illumina step ladder dilution chart, instead of using the latter chart itself.

File:

• extensions/net.sf.basedb.meludi/trunk/resources/libprep/select_dna_for_start_plate.js (modified) (4 diffs)

extensions/net.sf.basedb.meludi/trunk/resources/libprep/select_dna_for_start_plate.js

@@ -2335 +2335 @@
       {
         // Calculations for each aliquot
-        var VOL_ALIQUOT = 10.0; // µl
+        var VOL_ALIQUOT = 10.5; // µl
         var deltaCt = info.deltaCt;
         var dilutionFactor = painter.fetchDilutionFactor(deltaCt);
@@ -2413 +2413 @@
         if (info.QubitConc != null)
         {
-          text += '<div class="volumes"><span class="volume">'+Numbers.formatNumber(volDNA, 1)+'</span> + <span class="water">'+Numbers.formatNumber(water, 1)+'µl</span></div>';
+          text += '<div class="volumes"><span class="volume">'+Numbers.formatNumber(volDNA, 2)+'</span> + <span class="water">'+Numbers.formatNumber(water, 2)+'µl</span></div>';
         }
         // --- ΔCt
         if (info.deltaCt != null)
         {
-          text += '<div class="quality-score">ΔCt='+Numbers.formatNumber(info.deltaCt, 1) + '</div>';
+          text += '<div class="quality-score">ΔCt='+Numbers.formatNumber(info.deltaCt, 2) + '</div>';
           if (info.deltaCt > QUALITY_SCORE_WARNING_LIMIT) warningMsg[warningMsg.length] = 'High ΔCt value';
         }
@@ -2586 +2586 @@
   {
     var dilutionFactor = 1.0;
+/*
+    // Illumina ladder dilution chart
     if (deltaCt > 0.5 && deltaCt <= 1.5)
     {
@@ -2601 +2603 @@
     {
       dilutionFactor = 16.0;
+    }
+*/
+    // Dilution curve fitted to centers of ladder steps in Illumina ladder dilution chart (Mats Jönsson 2015-09-28)
+    var fact = 2.8284271247;
+    var expFact = 0.6931471806;
+    dilutionFactor = fact * Math.exp(-expFact*deltaCt);
+    if (dilutionFactor < 1.0)
+    {
+      dilutionFactor = 1.0;
     }
     return dilutionFactor;