[BioC] Defining Weights in marrayNorm.

Wed Aug 6 16:11:50 MEST 2003

I'm not quite sure, if it's true.  I changed your example a little bit:

> tst <- function(x, y=NULL) x + y
> tst(4, y=2)
[1] 6
> tst(4)
numeric(0)
> tmp <- function(x, ...) tst(x, y=NULL)
> tmp(4, y=2)
numeric(0)
> tmp <- function(x, ...) tst(x, y=3)
> tmp(4, y=2)
[1] 7

Apparently, y is not overwritten when you call tmp(). However, the following 
works fine:

> tmp <- function(x, ...) tst(x, ...)
> tmp(4, y=3)
[1] 7

Johannes

Zitiere James MacDonald <jmacdon at med.umich.edu>:

> 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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> > >Bioconductor at stat.math.ethz.ch 
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> > >
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> 
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