computePMAtable: Prepare and return a table of PMA calls

In ammar257ammar/ArrayAnalysis-Bioconductor: ArrayAnalysis

Prepare and return a table of PMA calls

Description

This function (from functions_processing) computes a table of Absent (A), Marginal (M), Present (P) calls based on the MAS5 function (affy package). This function will only work for chiptypes that have mismatch probes and for which the detection.p.val ( simpleaffy Bioconductor package) function that it calls works. A try construction will be used and if no table can be created a warning is given. Note that this function will always use the MAS5 algorithm, regardless of the normalization method used in the normalizeData function. In case customCDF is TRUE, annotation is updated using BrainArray custom cdf environments, before proceeding with the normalization (and summarisation of probe expressions into probeset expressions). To update the annotation, a sub call is made to the addUpdatedCDFenv function.

Usage

computePMAtable(Data, customCDF = TRUE, species = NULL, CDFtype = NULL)

Arguments

Data	(Status: required) The raw data object (datatype: AffyBatch)
customCDF	(Status: optional, Default: TRUE) Should annotation of the chip be updated before normalizing the data (and building the probesets out of the separate probes)? If requested, this is done using BrainArray updated cdf environments, c.f. addUpdatedCDFenv (datatype: logical)
species	(Status: required when customCDF is TRUE, c.f. addUpdatedCDFenv, Default: NULL)The species associated with the chip type. (datatype: character)
CDFtype	(Status: required when customCDF is TRUE, c.f. addUpdatedCDFenv, Default: NULL) The type of custom cdf requested. (datatype: character)

Value

A data.frame table called ‘PMAtable’ containing the PMA values for each probeset and array

Examples

#By default, the script will call, if customCDF is TRUE:
#PMAtable <- computePMAtable(rawData,customCDF,species,CDFtype)
#or, if customCDF is FALSE:
#PMAtable <- computePMAtable(rawData,customCDF)
#After this call, the main script will save the result
#to a tab-delimited text file, called PMAtable.txt

ammar257ammar/ArrayAnalysis-Bioconductor documentation built on Jan. 29, 2024, 7:21 a.m.