[BioC] Defining Weights in marrayNorm.

James MacDonald jmacdon at med.umich.edu
Mon Aug 4 14:26:44 MEST 2003

>From perusing the functions (particularly maNorm), it appears that the
weights are used by all normalization procedures except for "median". By
definition, a weight is in the range [0,1], so if you use 0 and 1, it
will effectively be the same as saying "don't use this" or "use this".
You can also use some more moderate values rather than completely
eliminating the 'bad' spots (e.g., simply down-weight spots that look

I think you pass the weights using the additional argument w="maW" in
your call to maNorm.



James W. MacDonald
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109

>>> "Josef Walker" <josef.walker at jenner.ac.uk> 08/04/03 12:31PM >>>
Hi all,


My name is Joe Walker and I am a final year PhD student attempting to
use Bioconductor to analyse a large amount of cDNA microarray data
my thesis experiments.


For the normalisation stage, there is the option to use weights
previously assigned to the genes. 

I wish to normalise my genes based on a quality controlled subset that
changes fro each hybridisation, I think one way to do this is to use
weights option during normalistion.

The "slot" for the weights (maW) is assigned/loaded during the
marrayInput stage using the read.marrayRaw command (along with name.Gf

What I am unclear of is:

1)       What form do these weights take i.e does 1 = use this gene
0 = do not use this gene, are they graded, or do they have to be

2)       Do you use these weights by simply using maW = TRUE, during
normalisation stage?


Am I at least on the right track?

If anyone has advice for me it would be great.


Thanks in advance,





Josef Walker BSc (Hons)

PhD Student

Memory Group

The Edward Jenner Institute for Vaccine Research


Nr Newbury


RG20 7NN


Tel: 01635 577905

Fax: 01635 577901

E-mail: Josef.walker at jenner.ac.uk 


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