Changeset 1113 for plugins/base2

Timestamp:

Jun 9, 2009, 12:14:07 AM (14 years ago)

Author:

Jari Häkkinen

Message:

Addresses #227

File:

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

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

@@ -11 +11 @@
 This plug-in implements !BeadStudio like detection P-value calculations
 for Illumina expression data (see
-http://www.genomecenter.ucdavis.edu/expression_analysis/documents/GEX__normalization_070313.pdf
+http://www.genomecenter.ucdavis.edu/expression_analysis/documents/illumina_normalization_081201.pdf)
 on detection P-values.
 
 The plug-in will ''always'' base the detection P-value calculation on
 raw data values, ''i.e.'', the mean raw intensity for the different
-bead types. However, only reporters included in the bioassay set will
-be included in the distributions. The effect of the reporter filtering
-that may have occurred is that if no negative control bead types are
-left in the bioassay set, there is no distribution of negative
-controls to base the P-value detection calculation on.
+signals. However, only reporters included in the bioassay set will be
+included in the calculations. This means that if there are no negative
+control bead types are left in the bioassay set, there is no
+distribution of negative controls to base the P-value detection
+calculation on. Or, if there are too few negative controls the
+detection P-value calculation is unreliable. (There is a request,
+http://baseplugins.thep.lu.se/ticket/204, for an user selectable
+option to use all available negative controls available in raw data
+irrespective the probe filtering state of the bio assayset.)
 
-Hence, typically you should use the detection P-value plug-in before
-you remove the negative controls from your analysis.
+Hence, always use the detection P-value plug-in before removing
+negative controls.
 
-There is a request, http://baseplugins.thep.lu.se/ticket/204, for an
-user selectable option to use all available negative controls in raw
-data even if no negative controls are left in a bioassay set.
+The detection P-value plug-in does not filter the assays, it provides
+the detection P-values usable in a filter step after running this
+plug-in.
+
+=== Parameters ===
+
+The plug-in requires input of array type since detection P-values
+depends on array type.
+
+The user can also set a cut off parameter to exclude outliers within
+the negative controls. The `cutoff` defines the acceptable negative
+control signal range
+{{{
+median-MAD*cutoff < I < median+MAD*cutoff
+}}}
+where `MAD` is the median absolute deviation.
+
+
+=== Implementation details ===
+
+Each assay is treated separately, i.e., no samples are combined
+together.
+
+Retrieve the raw expression value for all negative controls in the
+current bioassay set.
+
+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.
+
 
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