Changeset 1114 for plugins/base2/net.sf.basedb.illumina/trunk/README_PluginDetails

Timestamp:

Jun 10, 2009, 12:09:36 AM (14 years ago)

Author:

Jari Häkkinen

Message:

Addresses #113. The Pvalue calculation is in place. Need to figure details of std and average calculations.

File:

• plugins/base2/net.sf.basedb.illumina/trunk/README_PluginDetails (modified) (1 diff)

plugins/base2/net.sf.basedb.illumina/trunk/README_PluginDetails

@@ -55 +55 @@
 current bioassay set.
 
+Whole genome beadchips:
+
 For all signals `i` calculate the detection P-value as
-`Pvalue = 1-i/N` where `i` is the rank of the signal relative to
-the negative controls and `N` is the number of negative controls.
+`Pvalue = 1-i/N` where `R` is the rank of the signal i relative to the
+negative controls and `N` is the number of negative controls.
+
+Others (DASL, miRNA, VeraCode DASL, and Focused Arrays):
+
+For all signals `i` calculate the detection P-value as
+`Pvalue = 1/2 - erf( [i-AvgControl]/StdControl/sqrt(2) )` where
+`AvgControl` is the average intensity of the negative controls,
+`StdControl` is the standard deviation of the ... (to be defined and
+implemented accordingly), and `erf` is the error function
+(http://mathworld.wolfram.com/Erf.html). The error function is used
+for arguments witin the range (-4,4). To save CPU cycles, the function
+value for arguments outside this range is set to -1 and 1,
+respectively.