[BioC] Defining Weights in marrayNorm.

[James MacDonald]

I would think that because it appears to be true.

An example:

> tmp <- function(x, ...) tst(x, y=NULL)
> tst <- function(x, y=NULL) x + y
> tst(4, y=2)
[1] 6

Isn't the y=NULL being overwritten by the fact that I pass the variable
y=2?

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> 08/05/03 10:19AM >>>
At 11:07 PM 5/08/2003, James MacDonald wrote:
>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?

No. Why would you think that?

Gordon

>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]]
> >
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