Thank you so much for clarifying. It makes total sense. Neel On 10/18/11 11:44 AM, Sean Davis wrote: > Hi, Neel. > > Some rows have larger logFC than others. Without scaling, those rows > will be brighter than the rows that have smaller logFC. Scaling the > rows (columns) makes the rows (columns) have similar variation so that > even rows that have smaller logFC still have visible changes when > plotted. If most of your rows (columns) have similar variation, then > scaling will not make much difference. > > Sean > > On Tue, Oct 18, 2011 at 11:33 AM, Neel Aluru<naluru at="" whoi.edu=""> wrote: >> Hello Bioc Users, >> >> I am having a hard time understanding why heatmap.2 uses row (or column) >> Z-score instead of directly plotting logFC values? Based on the formula for >> calculating Z-score, I understand that it is used for scaling or smoothing. >> But, isn't it the same when using logFC. Please correct if I am wrong. I >> really appreciate if anyone can give me a clear explanation. >> >> Sorry for asking a silly question. I >> >> -- >> Neel Aluru >> Visiting Investigator >> Biology Department >> Woods Hole Oceanographic Institution >> 45 Woods Hole Road >> Woods Hole 02543 >> Massachusetts >> USA >> >> _______________________________________________ >> 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 >> -- Neel Aluru Visiting Investigator Biology Department Woods Hole Oceanographic Institution 45 Woods Hole Road Woods Hole 02543 Massachusetts USA