 Timestamp:
 Jun 9, 2009, 12:14:07 AM (14 years ago)
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plugins/base2/net.sf.basedb.illumina/trunk/README_PluginDetails
r1111 r1113 11 11 This plugin implements !BeadStudio like detection Pvalue calculations 12 12 for Illumina expression data (see 13 http://www.genomecenter.ucdavis.edu/expression_analysis/documents/ GEX__normalization_070313.pdf13 http://www.genomecenter.ucdavis.edu/expression_analysis/documents/illumina_normalization_081201.pdf) 14 14 on detection Pvalues. 15 15 16 16 The plugin will ''always'' base the detection Pvalue calculation on 17 17 raw data values, ''i.e.'', the mean raw intensity for the different 18 bead types. However, only reporters included in the bioassay set will 19 be included in the distributions. The effect of the reporter filtering 20 that may have occurred is that if no negative control bead types are 21 left in the bioassay set, there is no distribution of negative 22 controls to base the Pvalue detection calculation on. 18 signals. However, only reporters included in the bioassay set will be 19 included in the calculations. This means that if there are no negative 20 control bead types are left in the bioassay set, there is no 21 distribution of negative controls to base the Pvalue detection 22 calculation on. Or, if there are too few negative controls the 23 detection Pvalue calculation is unreliable. (There is a request, 24 http://baseplugins.thep.lu.se/ticket/204, for an user selectable 25 option to use all available negative controls available in raw data 26 irrespective the probe filtering state of the bio assayset.) 23 27 24 Hence, typically you should use the detection Pvalue plugin before25 you remove the negative controls from your analysis.28 Hence, always use the detection Pvalue plugin before removing 29 negative controls. 26 30 27 There is a request, http://baseplugins.thep.lu.se/ticket/204, for an 28 user selectable option to use all available negative controls in raw 29 data even if no negative controls are left in a bioassay set. 31 The detection Pvalue plugin does not filter the assays, it provides 32 the detection Pvalues usable in a filter step after running this 33 plugin. 34 35 === Parameters === 36 37 The plugin requires input of array type since detection Pvalues 38 depends on array type. 39 40 The user can also set a cut off parameter to exclude outliers within 41 the negative controls. The `cutoff` defines the acceptable negative 42 control signal range 43 {{{ 44 medianMAD*cutoff < I < median+MAD*cutoff 45 }}} 46 where `MAD` is the median absolute deviation. 47 48 49 === Implementation details === 50 51 Each assay is treated separately, i.e., no samples are combined 52 together. 53 54 Retrieve the raw expression value for all negative controls in the 55 current bioassay set. 56 57 For all signals `i` calculate the detection Pvalue as 58 `Pvalue = 1i/N` where `i` is the rank of the signal relative to 59 the negative controls and `N` is the number of negative controls. 60 30 61 31 62 
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