Hi, I'm a PhD student at Cardiff University, working on neuropsychiatric conditions by using clustering techniques on microarray data. I've dug through the archives, but haven't been able to find a definite answer to my question. When using justRMA to process microarray data from CEL files, when is the log2 transformation applied? Does it occur as part of the normalisation or background correction steps, and so will not occur if 'normalization=FALSE' or 'background=FALSE' is used? Or is it an inherent part of the process? I believe it's the latter, but I don't know for sure. Thanks very much, Alex Richards

The log2 transformation happens after background and normalization during the summarization stage. Turning normalization=FALSE or background=FALSE or both FALSE will have no effect on whether it gets log2 transformed. Best, Ben On Fri, 2007-03-16 at 11:53 +0000, Alexander Richards wrote: > Hi, > > I'm a PhD student at Cardiff University, working on neuropsychiatric conditions by using clustering > techniques on microarray data. I've dug through the archives, but haven't been able to find a > definite answer to my question. > > When using justRMA to process microarray data from CEL files, when is the log2 transformation > applied? Does it occur as part of the normalisation or background correction steps, and so will not > occur if 'normalization=FALSE' or 'background=FALSE' is used? Or is it an inherent part of the > process? I believe it's the latter, but I don't know for sure. > > Thanks very much, > > Alex Richards > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor

Hi Alexander, Alexander Richards wrote: > Hi, > > I'm a PhD student at Cardiff University, working on neuropsychiatric conditions by using clustering > techniques on microarray data. I've dug through the archives, but haven't been able to find a > definite answer to my question. > > When using justRMA to process microarray data from CEL files, when is the log2 transformation > applied? Does it occur as part of the normalisation or background correction steps, and so will not > occur if 'normalization=FALSE' or 'background=FALSE' is used? Or is it an inherent part of the > process? I believe it's the latter, but I don't know for sure. You _could_ just run justRMA() on some celfiles with normalize = FALSE and background = FALSE to see for yourself. But since you asked, it is an inherent part of the process. You wouldn't want to do medianpolish on unlogged data. Best, Jim > > Thanks very much, > > Alex Richards > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > 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 Affymetrix and cDNA Microarray Core University of Michigan Cancer Center 1500 E. Medical Center Drive 7410 CCGC Ann Arbor MI 48109 734-647-5623 ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues.