Does anyone have any R scripts they would like to share that would do diagnositics and normalizations for one-color oligo slides, such as Mergen and Amersham Codelink? I would like to do multi-array normalization. Thanks much, Dick ********************************************************************** ********* Richard P. Beyer, Ph.D. University of Washington Tel.:(206) 616 7378 Environmental Health, Box 354695 Fax: (206) 685 4696 4225 Roosevelt Way NE, # 100 Seattle, WA 98105-6099 ********************************************************************** *********

you can try the normalizations available in the affy package. although they are methods for the AffyBatch class, they all use engine functions that work on arbitrary matrices. On Thu, 30 Jan 2003, Dick Beyer wrote: > Does anyone have any R scripts they would like to share that would do diagnositics and normalizations for one-color oligo slides, such as Mergen and Amersham Codelink? > > I would like to do multi-array normalization. > > Thanks much, > Dick > ******************************************************************** *********** > Richard P. Beyer, Ph.D. University of Washington > Tel.:(206) 616 7378 Environmental Health, Box 354695 > Fax: (206) 685 4696 4225 Roosevelt Way NE, # 100 > Seattle, WA 98105-6099 > ******************************************************************** *********** > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > http://www.stat.math.ethz.ch/mailman/listinfo/bioconductor >

Hi, I had a sketch for a (more) general package to deal with oligo arrays. Althought it was for home-made oligoarrays, it could include the one you mention pretty easily. You can contact me off-list (or anybody else with interest in that). I believe we can have something in a wink. L.

Hi Dick, the 'vsn' package does normalization and variance stabilizing transformation on arbitrary matrices (i.e. rows=probes and columns=arrays). See the paper and the vignette for details. It works well for one-color spotted array data (and also for radioactive membranes.) Best regards Wolfgang Wolfgang Huber DKFZ Heidelberg, Germany On Thu, 30 Jan 2003, Dick Beyer wrote: > Does anyone have any R scripts they would like to share that would do diagnositics and normalizations for one-color oligo slides, such as Mergen and Amersham Codelink? > > I would like to do multi-array normalization. > > Thanks much, > Dick