[BioC] Defining Weights in marrayNorm.

[James MacDonald]

>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
sketchy).


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

HTH,

Jim



James W. MacDonald
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109
734-647-5623

>>> "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
from
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
the
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
etc).

What I am unclear of is:

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

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

 

Am I at least on the right track?

If anyone has advice for me it would be great.

 

Thanks in advance,

 

Joe

 

 

Josef Walker BSc (Hons)

PhD Student

Memory Group

The Edward Jenner Institute for Vaccine Research

Compton

Nr Newbury

Berkshire

RG20 7NN

 

Tel: 01635 577905

Fax: 01635 577901

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

 


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