[BioC] Normalization with cDNA array, Bioconductor Digest, Vol 11, Issue 44

Christopher Wilkinson Christopher.Wilkinson at adelaide.edu.au
Mon Feb 2 04:08:45 MET 2004

> Message: 1
> Date: Fri, 30 Jan 2004 09:02:04 -0600
> From: Joyce Gu <jwgu at bcm.tmc.edu>
> Subject: [BioC] Normalization with cDNA array

> Hello,
> There are two ways to normalize the data, one is location normalization, the 
> other is scale normalization in marrayClasses. I am wondering what kind of 
> situation should we use location normalization,and when should we use scale 
> normalization? 
> Does anyone has any suggession?

The choice of normalisation method usually depends upon the quality of
the data. With cDNA arrays you generally want to remove dye bias effects
along with any spatial effects, so print-tip loess normalisation is
generally advised (method=PrintTipLoess in maNorm). If some of the
print-tip groups still have a large spread compared to other print-tip
groups on the array (look at the box plots of M values) you can use
scale normalisation to correct for this (assuming the effect isn't due
to a large number of DE genes in those print-tip groups).

For a description of different normalisation methods have a look at

Smyth, G. K., and Speed, T. P. (2003). Normalization of cDNA microarray
data. In: METHODS: Selecting Candidate Genes from DNA Array Screens:
Application to Neuroscience, D. Carter (ed.). Methods Volume 31, Issue
4, December 2003, pages 265-273.


Yang, Y. H., Dudoit, S., Luu, P., Lin, D. M., Peng, V., Ngai, J., and
Speed, T. P. (2002). Normalization for cDNA microarray data: a robust
composite method addressing single and multiple slide systematic
variation. Nucleic Acids Research 30(4):e15.


Dr Chris Wilkinson

Research Officer (Bioinformatics)        | Visiting Research Fellow
Child Health Research Institute (CHRI)   | Microarray Analysis Group
7th floor, Clarence Rieger Building      | Room 121
Women's and Children's Hospital          | School of Applied Mathematics
72 King William Rd, North Adelaide, 5006 | The University of Adelaide,

Math's Office (Room 121)        Ph: 8303 3714
CHRI   Office (2nd floor)       Ph: 8161 6363

Christopher.Wilkinson at adelaide.edu.au


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