Zipf's Law Microarray Normalization
Introduction
This page accompanies our published description of a microarray normalization method
using Zipf's Law. A detailed description of the method can be found in the original paper:
Can Zipf's law be adapted to normalize microarrays?
Lu T, Costello CM, Croucher PJP, Haesler R, Deusch G, Schreiber S.
BMC Bioinformatics 2005, 6:37
Pubmed ID: 15727680
Sample data sets
Two data sets were described in the original article. These text files are tab
delimited and in the following format:
- Genes arranged in rows with gene annotations in the first column.
- Microarrays arranged in columns with the array name in the first row.
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Norm_CD_UC_data.txt
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- Microarray type:
Filter based cDNA from the RZPD
- Number of genes:
33,792
- Number of microarrays:
31
- Probed with:
Total RNA from human sigmoidal colon.
- Within microarray normalization:
None
|
|
rat_raw.txt
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- Microarray type:
Clonetech Atlas Rat cDNA 7738-1
- Number of genes:
558
- Number of microarrays:
33
- Probed with:
Total RND from rat cerebellum and olive.
- Within microarray normalization:
None
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|
Mouse_raw.dat
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- Microarray type:
Custom two-channel boutique microarray
- Number of genes:
447
- Number of microarrays:
5 (2 channels each)
- Probed with:
Total RNA from mouse cell lines.
- Within microarray normalization:
None
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Normalization software
Three implimentations of the Zipf's Law normalization have been developed, two are available for download.
Last updated: 07.03.2005