[BioC] Defining Weights in marrayNorm.

[Gordon Smyth]

At 11:46 PM 2/09/2003, Josef Walker wrote:
>Hi Gordon,
>
>Having spent time trying to do the weights thing in marrayNorm, I had a
>go at using the limma package and the instructions you give below. The
>weights thing seems to have worked (in my hands, a minor miracle!).
>
>I have a couple of question that I can't seem to get the answers to from
>the accompanying literature.
>
>1) When creating an RGlist from a genepix file, are the columns used for
>R, Rb, G and Gb the MEDIAN values or MEAN? I know it says I can specify
>them, but I'm not sure how.

R and G are means and Rb and Gb are medians. (The Genepix backgrounds are 
often larger than I'd like them to be, so I wouldn't recommend a change to 
mean backgrounds.)

In the latest (development) version of limma, there is an example showing 
how to change the columns used for Genepix data in Section 3 "Reading in 
Intensity Data" of the html limma User's Guide.

>2) Is there an option to carry out Within-arrays Scale and PrintTip
>normalisation as you can in marrayNorm?

There is no option for print-tip scale normalization. Print-tip scale 
normalization was not found to be effective in the original Yang et al 
paper. I have never seen a data set for which I think it's a good idea, so 
I don't provide it. Print-tip loess normalization is of course provided and 
is the default method.

All the best
Gordon

>Thanks in advance for your help.
>
>
>Joe
>
>Josef Walker BSc (Hons)
>PhD Student
>Memory Group
>The Edward Jenner Institute for Vaccine Research
>Compton
>Nr Newbury
>Berkshire
>RG20 7NN
>
>-----Original Message-----
>From: Gordon Smyth [mailto:smyth at wehi.edu.au]
>Sent: 06 August 2003 05:25
>To: michael watson (IAH-C)
>Cc: Josef Walker; bioconductor at stat.math.ethz.ch
>Subject: RE: [BioC] Defining Weights in marrayNorm.
>
>
>As I understand it, your spot flags are 0/1 and they are added as an
>extra
>column to your image analysis output file. If this is so and if the name
>of
>the extra column is "MyFlag" say, then doing what you want in limma is
>very
>simple. You simply add the argument
>
>     wt.fun = function(x) x$MyFlag
>
>when you read the data into R using read.maimages. That's it. Everything
>
>will work automatically - the weights be read in and will be used
>automatically for normalisation and for other analyses.