createNormDataTable: Prepare and export the normalized data table

In ammar257ammar/ArrayAnalysis-Bioconductor: ArrayAnalysis

Prepare and export the normalized data table

Description

This function (from functions_processing) prepares a table suitable for visualisation and saving to disk from a normalized data object. In case of use of an updated cdf annotation (customCDF is TRUE), it will remove the artificial “_at” postfixes from all probeset IDs, apart from the affx controls, in order to get the real IDs from the database used to create the update. Also, in case an updated cdf environment based on Ensemble Gene ID (“ENSG”) has been used, the function tries to connect to BioMart (using the biomaRt BioConductor package) in order to add two extra columns of information to the table: the common gene name, and a gene description. This will (for now) not be done for other updated cdf types, as there is no one-to-one mapping between BioMart entries and these IDs or it has not been sufficiently tested. Note that the BioMart connection may sometimes not be established (e.g. if the service is down or busy), it may in such cases be worthwhile to try again.

Usage

createNormDataTable(normData, customCDF = NULL, species = NULL, CDFtype = NULL)

Arguments

normData	(Status: required) The normalized data object (datatype: ExpressionSet)
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 with normalized data, and possible extra annotation.

Examples

#By default, the script will call:
#normDataTable <- createNormDataTable(normData, customCDF, species, CDFtype)
#After this function has been called, the normDataTable object is
#saved to a tab-delimited text file by the main script.

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