Hi Alberto, There has not been much in the literature (as you say) about normalizing single-channel data. I have been working on this, looking at combining two-channel approaches that allow the recovery of logR, logG single-channels (i.e pin-group lowess etc) plus approaches used for affymetrix normalisation (i.e quantile normalisation). In the following reference I wrote a small intro to the problem of normalising single-channel data from two-colour cDNA microrarrays with Jean. Normalization for Two-color cDNA Microarray Data Yee Hwa Yang and Natalie P. Thorne IMS Lecture Notes -- Monograph Series, Volume 40, 2003 Science and Statistics: A Festschrift for Terry Speed Editor: Darlene R. Goldstein The main reason the rest of my work hasn't been published is that I am in the last few months of finishing my PhD thesis (time issue!), but I plan to publish soon after that. My main focus is on the assessment of proposed single-channel normalisation methods. It sounds as though you may be using cDNA data which only has one colour. I haven't had any experience with this kind of data, but I would recommend you look at the quantile normalisation method (there is a routine in the R Limma package library) and think/look carefully how it is doing. We find it works quite well. If you do infact have two-colour data, try a pin-group normalisation on the M-values, then quantile normalise across slides the A-values. Then take Mp and Aq and recontruct logR and logG (pretty easy to figure out). Hope this helps. Natalie On Fri, 8 Aug 2003, Alberto Labarga wrote: > Dear Ms. Thorne, > > my name is Alberto Labarga, I work at university of Navarra, and I'm > studying normalization methods for single-channel microarray data (not > Affymetrix), becouse some people here are working with this technology, I > saw in your home page that you are working in this subject, and Dr. Remiers > also recommended to get in contact with you, could you give me some > references for this subject or any hint on which would be the best approach? > > thank you very much > > alberto > > > ----- Original Message ----- > From: "Mark Reimers" <mark.reimers@biosci.ki.se> > To: "Alberto Labarga" <alberto.labarga@unavarra.es> > Cc: "Natalie Thorne" <thorne@wehi.edu.au> > Sent: Friday, August 08, 2003 1:17 PM > Subject: Re: microarray normalization > > > > Hi Alberto, > > for single-channel cDNA array I suggest you get in touch with Natalie > > > > Natalie Thorne <thorne@wehi.edu.au> > > > who has done a lot on this. > > > > regards > > > > Mark > > > > On Fri, 2003-08-08 at 12:36, Alberto Labarga wrote: > > > Dear DR. Reimers, > > > > > > I have seen that one of your research interest is normalization of > > > single channel microarrays, I have seen that much of the literature is > > > about two-color microarrays, but in our center (university of navarra, > > > spain) we are doing single-channel (not Affymetrix), and we are trying > > > to find a good normalization method, > > > > > > could you give me some references for this subject? > > > thank you very much > > > > > > alberto > > -- > > Mark Reimers > > Assistant Professor, Biosciences, and > > Statistical Expert, Bioinformatics and Expression Analysis Facility, > > Karolinska Institute > > Stockholm > > > > > > >