genes.rpt.agi {Agi4x44PreProcess}R Documentation

Genes interrogated for different probes

Description

Some Genes are interrogated by different probes at different positions. This function identifies different probes interrogating the same gene. This group of probes is called a GENE SET.

Usage

genes.rpt.agi(dd, annotation.package, raw.data, WRITE.html, REPORT)

Arguments

dd An RGList: raw data or Processed data
annotation.package a character specifying the AGI annotation package: 'hgug4112a.db','mgug4122a.db'
raw.data logical, if TRUE it uses RAW data, otherwise it uses PROCESSED data
WRITE.html logical, if TRUE it writes an html output
REPORT logical, if TRUEit generates an information REPORT

Value

Generates an 'html' file and a 'txt' file with information about genes that are interrogated for different probes at different chr positions. The 'html' file includes a link to the ENSEMBL data base, exactly to the chr region where the 60 base agilent probe claims to be located. Chr coordinates are taken directly from the agilent files (data files obtained after image scanning and using Agilent Feature Extraction)

Author(s)

Pedro Lopez-Romero

Examples

        data(dd)
        library(hgug4112a.db)
        genes.rpt.agi(dd,"hgug4112a.db",raw.data=TRUE,
                WRITE.html=TRUE,REPORT=TRUE)


[Package Agi4x44PreProcess version 1.2.0 Index]