Hi Jim, Thank you. Does this mean that I can obtain the desired normalization by the following? mas5(data.MRW, normalize=FALSE, sc=50) Matthew ----------------------------------------------------- Matthew R. Willmann, Ph.D. Research Associate, Poethig Lab University of Pennsylvania Department of Biology 433 S. University Avenue Philadelphia, PA 19104 Lab phone: 215-898-8916 Cell: 508-243-2495 Fax: 215-898-8780 On Dec 6, 2010, at 3:55 PM, James W. MacDonald wrote: > Hi Matthew, > > On 12/6/2010 11:16 AM, Matthew Willmann wrote: >> Hello, >> >> I am trying to replicate results in a published paper, where they performed a MAS5.0 normalization with the median normalized to 50 and then defined genes as present if the normalized expression value is higher than 30. Does anyone know how I can alter the standard code to establish these parameters? >> >>> Cel.files=list.files(pattern=".CEL") >>> data.MRW=ReadAffy(filenames=Cel.files) >>> mas5(data.MRW, normalize=TRUE, sc=500) > > From the help page for mas5(): > > Usage: > > mas5(object, normalize = TRUE, sc = 500, analysis = "absolute", ...) > > Arguments: > > object: an instance of 'AffyBatch' > > normalize: logical. If 'TRUE' scale normalization is used after we > obtain an instance of 'ExpressionSet' > > So if you use mas5() with normalize = FALSE, then you don't get any scale normalization. You can then simply scale each chip to have a median of 50. > > Best, > > Jim > > >> >> Thank you for your time and advice. >> >> >> Matthew >> >> >> >> ----------------------------------------------------- >> Matthew R. Willmann, Ph.D. >> Research Associate, Poethig Lab >> University of Pennsylvania >> Department of Biology >> 433 S. University Avenue >> Philadelphia, PA 19104 >> Lab phone: 215-898-8916 >> Cell: 508-243-2495 >> Fax: 215-898-8780 >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at r-project.org >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > > -- > James W. MacDonald, M.S. > Biostatistician > Douglas Lab > University of Michigan > Department of Human Genetics > 5912 Buhl > 1241 E. Catherine St. > Ann Arbor MI 48109-5618 > 734-615-7826 > ********************************************************** > Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues >