[BioC] Defining Weights in marrayNorm.

[michael watson (IAH-C)]

Hi

I think the problem that both Jo and myself are having is that we want to know how to subset data, either in limma or the marray* classes, such that we only use good quality spots in the normalisation process.  

The problem is, the spots that are "good quality" differ from array to array, so it's not something we can set in the layout object unless we create a different layout object for each array.  So we started looking at the concept of using "weights", but really, the problem of not being able to subset our data successfully still remains.

So as a more generalised question, how can I use Bioconductor to normalise microarray data based only on a subset of good quality spots, the location of which will differ from array to array?

Thanks
M

-----Original Message-----
From: Gordon Smyth [mailto:smyth at wehi.edu.au]
Sent: 05 August 2003 01:26
To: James MacDonald
Cc: bioconductor at stat.math.ethz.ch; josef.walker at jenner.ac.uk
Subject: Re: [BioC] Defining Weights in marrayNorm.


Dear James and Jim,

Actually the maNorm function doesn't make use of weights, even though 
weights might be set in the marrayRaw object. If you look at the code for 
maNorm you will see that the weights are set to NULL when the call is main 
to maNormMain.

If you want to use weights for normalization you need either to use the 
lower level function maNormMain (which appears to use weights) or use the 
normalization routines in the limma package instead.

In limma you use read.maimages to read the data into, perhaps picking up 
the quality weights from genepix or quantarray in the process. If you have 
made your own weights, you can simply assign them to the weights component, 
e.g.,

RG <- read.maimages(files, source=your image analysis program)
RG$weights <- your.weights
RG$printer <- info about array layout, e.g., 
list=(ngrid.c=4,ngrid.r=4,nspot.r=20,nspot.c=20)
MA <- normalizeWithinArrays(RG)

Gordon

At 03:26 AM 5/08/2003, James MacDonald wrote:
> >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
>
>
>
>
>         [[alternative HTML version deleted]]
>
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