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@wehi.edu.au] >Sent: 06 August 2003 05:25 >To: michael watson (IAH-C) >Cc: Josef Walker; bioconductor@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.