Description Usage Arguments Details Value Author(s) References
View source: R/normalize.quantiles.exonarray.R
Performs a between-GeneChip quantile normalization for Affymetrix Exon microarrays or comparable GeneChips.
1 | normalize.quantiles.exonarray(x, use.log2=FALSE, verbose = TRUE)
|
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. |
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).
An AffyBatch object with quantile normalised intensity values (in natural scale).
Johannes Rainer
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
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