Hi, Does anyone know how the values in the DEGraph demo exprData matrix were calculated? I have read the DEGraph documentation, as well as the source documents for the data (GSE6532), and I can't figure out how to go from the RMA values (range 0-16) to the values in the exprData matrix (-5 to 7.5 about). It doesn't seem to be z-scores. If anyone can help, I'd love to hear. Just trying to understand the details of DEGraph Thanks very much, Dick ********************************************************************** ********* Richard P. Beyer, Ph.D. University of Washington Tel.:(206) 616 7378 Env. & Occ. Health Sci. , Box 354695 Fax: (206) 685 4696 4225 Roosevelt Way NE, # 100 Seattle, WA 98105-6099 http://depts.washington.edu/ceeh/members_fc_bioinfo.html http://staff.washington.edu/~dbeyer

Hi Dick, > > > Hi, > > Does anyone know how the values in the DEGraph demo exprData matrix were > calculated? ?I have read the DEGraph documentation, as well as the source > documents for the data (GSE6532), and I can't figure out how to go from the > RMA values (range 0-16) to the values in the exprData matrix (-5 to 7.5 > about). ?It doesn't seem to be z-scores. > > If anyone can help, I'd love to hear. ?Just trying to understand the details > of DEGraph Thanks for your interest in DEGraph. The (probe set) expression values from the demo were taken from the "LUMINAL.RData.gz" file in the GSE6532 GEO archive: ftp://ftp.ncbi.nih.gov/pub/geo/DATA/supplementary/series/GSE6532/LUMIN AL.RData.gz These files were processed by RMA, and *median-centered*, as explained in the corresponding README file (ftp://ftp.ncbi.nih.gov/pub/geo/DATA/supplementary/series/GSE6532/LUMI NAL_README.txt.gz): "RMA normalization was performed separately for each population ("series" in demo) and all the probesets were median centered." Note that 'population' refers to the fact that the data comes from three different institutions. This median-centering explains the range of expression values in "LUMINAL.RData", and therefore the range of the corresponding values in the demo data set of the DEGraph package. In case you'd like more information on what exactly is in DEGraph's 'exprData': the data in GSE6532 is at the *probe set* level and the data in DEGraph is at the *gene* level. We defined the expression level of a gene as the expression level of the probe set with largest alignment score among all probe sets mapping to this gene according to the annotation in GSE6532. When the largest alignment score was achieved by several probe sets, we took the median expression level of those probe sets. I've just posted the script we have been using to do this here: http://stat.genopole.cnrs.fr/_media/Members/pneuvial/Loi2008_geneLevel Data.R I hope this helps, Pierre > > Thanks very much, > Dick > ******************************************************************** *********** > Richard P. Beyer, Ph.D. University of Washington > Tel.:(206) 616 7378 ? ? Env. & Occ. Health Sci. , Box 354695 > Fax: (206) 685 4696 ? ? 4225 Roosevelt Way NE, # 100 > ? ? ? ? ? ? ? ? ? ? ? ?Seattle, WA 98105-6099 > http://depts.washington.edu/ceeh/members_fc_bioinfo.html > http://staff.washington.edu/~dbeyer > > _______________________________________________ > 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

Hi Pierre, Perfect! Thanks very much for your thorough explanation. Cheers, Dick ********************************************************************** ********* Richard P. Beyer, Ph.D. University of Washington Tel.:(206) 616 7378 Env. & Occ. Health Sci. , Box 354695 Fax: (206) 685 4696 4225 Roosevelt Way NE, # 100 Seattle, WA 98105-6099 http://depts.washington.edu/ceeh/members_fc_bioinfo.html http://staff.washington.edu/~dbeyer