[BioC] Defining Weights in marrayNorm.

[James MacDonald]

Hey Gordon,

I see that weights are set to null in maNormMain, but if you input
something like w="maW" in maNorm, doesn't that get passed as a variable
(using the ... portion of the function call), and override the w=NULL in
maNormMain?

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

>>> Gordon Smyth <smyth at wehi.edu.au> 08/04/03 08:25PM >>>
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]]
>
>_______________________________________________
>Bioconductor mailing list
>Bioconductor at stat.math.ethz.ch 
>https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor 
>
>_______________________________________________
>Bioconductor mailing list
>Bioconductor at stat.math.ethz.ch 
>https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor