Ignore:
Timestamp:
Jun 10, 2009, 11:41:55 PM (14 years ago)
Author:
Jari Häkkinen
Message:

Fixes #227.

File:
1 edited

Legend:

Unmodified
Added
Removed
  • plugins/base2/net.sf.basedb.illumina/trunk/README_PluginDetails

    r1114 r1122  
    3535=== Parameters ===
    3636
    37 The plug-in requires input of array type since detection P-values
    38 depends on array type.
     37The plug-in requires input of array type since detection P-value are
     38calculated differently depending on array type.
    3939
    4040The user can also set a cut off parameter to exclude outliers within
     
    5050
    5151Each assay is treated separately, i.e., no samples are combined
    52 together.
     52together. All calculations are made on the raw bead-type level data,
     53i.e., on the average expression value for each bead type and raw data
     54is always used irrespective when in analysis the detection P-value is
     55calculated.
    5356
    54 Retrieve the raw expression value for all negative controls in the
    55 current bioassay set.
    56 
    57 Whole genome beadchips:
     57Pvalue calculation for whole genome arrays:
    5858
    5959For all signals `i` calculate the detection P-value as
    60 `Pvalue = 1-i/N` where `R` is the rank of the signal i relative to the
     60`Pvalue = 1-R/N` where `R` is the rank of the signal `i` relative to the
    6161negative controls and `N` is the number of negative controls.
    6262
    63 Others (DASL, miRNA, VeraCode DASL, and Focused Arrays):
     63Pvalue calculation for others array types (DASL, miRNA, VeraCode DASL,
     64and Focused Arrays):
    6465
    6566For all signals `i` calculate the detection P-value as
    6667`Pvalue = 1/2 - erf( [i-AvgControl]/StdControl/sqrt(2) )` where
    6768`AvgControl` is the average intensity of the negative controls,
    68 `StdControl` is the standard deviation of the ... (to be defined and
    69 implemented accordingly), and `erf` is the error function
     69`StdControl` is the standard deviation of the the negative controls,
     70and `erf` is the error function
    7071(http://mathworld.wolfram.com/Erf.html). The error function is used
    71 for arguments witin the range (-4,4). To save CPU cycles, the function
     72for arguments within the range (-4,4). To save CPU cycles, the function
    7273value for arguments outside this range is set to -1 and 1,
    7374respectively.
     
    7677----------------------------------------------------------------------
    7778{{{
    78 
    7979Copyright (C) 2009 Jari Häkkinen
    8080
Note: See TracChangeset for help on using the changeset viewer.