 Timestamp:
 Jun 10, 2009, 11:41:55 PM (14 years ago)
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plugins/base2/net.sf.basedb.illumina/trunk/README_PluginDetails
r1114 r1122 35 35 === Parameters === 36 36 37 The plugin requires input of array type since detection Pvalue s38 dependson array type.37 The plugin requires input of array type since detection Pvalue are 38 calculated differently depending on array type. 39 39 40 40 The user can also set a cut off parameter to exclude outliers within … … 50 50 51 51 Each assay is treated separately, i.e., no samples are combined 52 together. 52 together. All calculations are made on the raw beadtype level data, 53 i.e., on the average expression value for each bead type and raw data 54 is always used irrespective when in analysis the detection Pvalue is 55 calculated. 53 56 54 Retrieve the raw expression value for all negative controls in the 55 current bioassay set. 56 57 Whole genome beadchips: 57 Pvalue calculation for whole genome arrays: 58 58 59 59 For all signals `i` calculate the detection Pvalue as 60 `Pvalue = 1 i/N` where `R` is the rank of the signal irelative to the60 `Pvalue = 1R/N` where `R` is the rank of the signal `i` relative to the 61 61 negative controls and `N` is the number of negative controls. 62 62 63 Others (DASL, miRNA, VeraCode DASL, and Focused Arrays): 63 Pvalue calculation for others array types (DASL, miRNA, VeraCode DASL, 64 and Focused Arrays): 64 65 65 66 For all signals `i` calculate the detection Pvalue as 66 67 `Pvalue = 1/2  erf( [iAvgControl]/StdControl/sqrt(2) )` where 67 68 `AvgControl` is the average intensity of the negative controls, 68 `StdControl` is the standard deviation of the ... (to be defined and69 implemented accordingly),and `erf` is the error function69 `StdControl` is the standard deviation of the the negative controls, 70 and `erf` is the error function 70 71 (http://mathworld.wolfram.com/Erf.html). The error function is used 71 for arguments wit in the range (4,4). To save CPU cycles, the function72 for arguments within the range (4,4). To save CPU cycles, the function 72 73 value for arguments outside this range is set to 1 and 1, 73 74 respectively. … … 76 77  77 78 {{{ 78 79 79 Copyright (C) 2009 Jari Häkkinen 80 80
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