Changeset 1122 for plugins/base2/net.sf.basedb.illumina/trunk/README_PluginDetails

Timestamp:

Jun 10, 2009, 11:41:55 PM (14 years ago)

Author:

Jari Häkkinen

Message:

Fixes #227.

File:

• plugins/base2/net.sf.basedb.illumina/trunk/README_PluginDetails (modified) (3 diffs)

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

@@ -35 +35 @@
 === Parameters ===
 
-The plug-in requires input of array type since detection P-values
-depends on array type.
+The plug-in requires input of array type since detection P-value are
+calculated differently depending on array type.
 
 The user can also set a cut off parameter to exclude outliers within
@@ -50 +50 @@
 
 Each assay is treated separately, i.e., no samples are combined
-together.
+together. All calculations are made on the raw bead-type level data,
+i.e., on the average expression value for each bead type and raw data
+is always used irrespective when in analysis the detection P-value is
+calculated.
 
-Retrieve the raw expression value for all negative controls in the
-current bioassay set.
-
-Whole genome beadchips:
+Pvalue calculation for whole genome arrays:
 
 For all signals `i` calculate the detection P-value as
-`Pvalue = 1-i/N` where `R` is the rank of the signal i relative to the
+`Pvalue = 1-R/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):
+Pvalue calculation for others array types (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
+`StdControl` is the standard deviation of the the negative controls,
+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
+for arguments within the range (-4,4). To save CPU cycles, the function
 value for arguments outside this range is set to -1 and 1,
 respectively.
@@ -76 +77 @@
 ----------------------------------------------------------------------
 {{{
-
 Copyright (C) 2009 Jari Häkkinen