Jianping, Thank you for getting back to me, I do set all of the array column headers to 1 as all of the biological comparisons are the same in the same ratio orientation. It has to do with the number of columns of data in total on the worksheet, it only likes odd numbers of arrays. Liz -----Original Message----- From: Jianping Jin [mailto:jjin@email.unc.edu] Sent: Friday, January 05, 2007 8:25 AM To: Brooke-Powell, Elizabeth; bioconductor at stat.math.ethz.ch Subject: Re: [BioC] Oneclass SAM analysis Hi Elizabeth, Did you set every measurement equal to 1s (not 1s and 2s)? As I understand one class analysis tests whether the mean gene expression across all replicates differs from zero. There is no any group comparison involved. If you were trying to do groups 1 and 2 comparison you probably need a "two-class" test. hope this helps Jianping

A one-class test is correct if the data are the log expression ratios (M). --Naomi At 09:24 AM 1/5/2007, Jianping Jin wrote: >Hi Elizabeth, > >Did you set every measurement equal to 1s (not 1s and 2s)? As I understand >one class analysis tests whether the mean gene expression across all >replicates differs from zero. There is no any group comparison involved. If >you were trying to do groups 1 and 2 comparison you probably need a >"two-class" test. > >hope this helps > >Jianping > > >--On Thursday, January 04, 2007 3:22 PM -0600 "Brooke-Powell, Elizabeth" ><etbp2 at="" borcim.wustl.edu=""> wrote: > > > Dear list, > > > > I am wondering if you would be able help me with a problem I seem to be > > experiencing using SAM (v2.20a). I am using it through the Excel add-in, > > but the question I have is not a technical computer or programming > > problem (to my knowledge) but one about the analysis itself. > > > > When I am performing oneclass analysis of ratio data from a microarray > > experiment it seems that the oneclass analysis only likes to have odd > > numbers of data columns where each data column is a list of ratios for one > > slide in an experiment. I can get analysis done for 3,5,7,9,and 11 slides > > of data, but not 2,4,6,8,10 or 12. I am wondering if I am missing > > something about oneclass analysis, but it seems to me that you would want > > a balanced design of an experiment with even numbers of slides. > > > > Any help would be appreciated, I have tried contacting the SAM list which > > is next to useless. > > > > Happy New Year to everyone, > > > > Liz Brooke-Powell > > > > Washington University Medical School, > > Department of Molecular Microbiology, > > CB#8230, 660 S. Euclid Ave > > St. Louis, MO, 63110 > > > > _______________________________________________ > > 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 > > > >################################## >Jianping Jin Ph.D. >Bioinformatics scientist >Center for Bioinformatics >Room 3133 Bioinformatics building >CB# 7104 >University of Chapel Hill >Chapel Hill, NC 27599 >Phone: (919)843-6105 >FAX: (919)843-3103 >E-Mail: jjin at email.unc.edu > >_______________________________________________ >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 Naomi S. Altman 814-865-3791 (voice) Associate Professor Dept. of Statistics 814-863-7114 (fax) Penn State University 814-865-1348 (Statistics) University Park, PA 16802-2111