BASH
(Package: beadarray) :
BASH - BeadArray Subversion of Harshlight
BASH is an automatic detector of physical defects on an array. It is designed to detect three types of defect - COMPACT, DIFFUSE and EXTENDED.
● Data Source:
BioConductor
● Keywords: misc
● Alias: BASH
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BASHCompact
(Package: beadarray) :
BASH - Compact Defect Analysis
Creates a list of probes marked as being in compact defects.
● Data Source:
BioConductor
● Keywords: misc
● Alias: BASHCompact
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BASHDiffuse
(Package: beadarray) :
BASH - Diffuse Defect Analysis
Creates a list of probes marked as being in diffuse defects.
● Data Source:
BioConductor
● Keywords: misc
● Alias: BASHDiffuse
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BASHExtended
(Package: beadarray) :
BASH - Extended Defect Analysis
Returns a score, which assesses the extent to which the background is changing across the array/strip.
● Data Source:
BioConductor
● Keywords: misc
● Alias: BASHExtended
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Following the guidelines at http://www.ncbi.nlm.nih.gov/geo/info/geo_illu.html, we provide functionality to create the three types of file required for a GEO submission of Illumina expression data. These are 1) sample metadata 2) Normalised intensities 3) Raw intensities.
● Data Source:
BioConductor
● Keywords:
● Alias: createGEOMatrix, createGEOMeta, makeGEOSubmissionFiles
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Template containing latest required fields for GEO submission
● Data Source:
BioConductor
● Keywords:
● Alias: metaTemplate
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HULK
(Package: beadarray) :
HULK - Bead Array Normalization by NEighbourhood Residuals
Normalizes an probe intensities by calculating a weighted average residual based on the residuals of the surrounding probes.
● Data Source:
BioConductor
● Keywords: misc
● Alias: HULK
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Adds extra probe-specific data to an ExpressionSetIllumina object using an installed annotation package
● Data Source:
BioConductor
● Keywords:
● Alias: addFeatureData
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An interface to set or retrieve information about the annotation of a beadLevelData or ExpressionSetIllumina object.
● Data Source:
BioConductor
● Keywords:
● Alias: annotation, annotation,ExpressionSetIllumina-method, annotation,beadLevelData-method, annotation<-,ExpressionSetIllumina,character-method, annotation<-,beadLevelData,character-method, getControlProfile, suggestAnnotation
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Function to perform a basic bead-level background correction using a defined set of foreground and background intensities.
● Data Source:
BioConductor
● Keywords:
● Alias: backgroundCorrectSingleSection
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providing 
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