normalize.quantiles.exonarray: Quantile normalization for Exon microarrays

In jotsetung/generalgcrma: GCRMA background adjustment for Affymetrix Tiling, Exon and Gene ST microarrays.

Description

Performs a between-GeneChip quantile normalization for Affymetrix Exon microarrays or comparable GeneChips.

Usage

normalize.quantiles.exonarray(x, use.log2=FALSE, verbose = TRUE)

Arguments

x	The AffyBatch object.
use.log2	If the quantile normalisation should be performed in log2 scale rather than natural scale. Note that the returned normalized intensities are in natural scale.
verbose	If additional messages should be printed.

Details

Affymetrix Exon microarrays contain probes that target individual Exons of gene transcripts. Depending on the type of analysis (e.g. summarise per transcript probes, or per-gene-probes) probes can be part of several probe sets (i.e. for transcripts of a gene sharing some exons). This function performs the quantile preprocessing on the intensities of all unique pm probes (the normalize.quantiles function from the preprocessCore package would consider the non-unique set of pm probes, i.e. for transcript probe set definitions the probe sets targeting transcripts of the same gene share usually a large number of probes).

Value

An AffyBatch object with quantile normalised intensity values (in natural scale).

Author(s)

Johannes Rainer

References

Rainer J, Lelong J, Bindreither D, Mantinger C, Ploner C, Geley S, Kofler R. (2012) Research resource: transcriptional response to glucocorticoids in childhood acute lymphoblastic leukemia. Mol Endocrinol. 2012 Jan;26(1):178-93.

http://bioinfo.i-med.ac.at

jotsetung/generalgcrma documentation built on May 19, 2019, 9:41 p.m.