When you use the scaling capabilities of heatmap.2, the resulting plot heatmap shows a legend that says "Column Z scores" or "Row Z scores". The scaling looks as though the values have been normalized to SD units. z = (x - mean)/sd Is this what heatmap.2 means by a Z score? I am finding it tricky to reproduce their results using the z value above. Best, Tom

Hi Tom, Thomas Hampton wrote: > When you use the scaling capabilities of heatmap.2, the > resulting plot heatmap shows a legend that says > > "Column Z scores" or > > "Row Z scores". > > The scaling looks as though the values have been normalized > to SD units. > > z = (x - mean)/sd > > Is this what heatmap.2 means by a Z score? Yes. From the code for heatmap.2(): if (scale == "row") { retval$rowMeans <- rm <- rowMeans(x, na.rm = na.rm) x <- sweep(x, 1, rm) retval$rowSDs <- sx <- apply(x, 1, sd, na.rm = na.rm) x <- sweep(x, 1, sx, "/") } else if (scale == "column") { retval$colMeans <- rm <- colMeans(x, na.rm = na.rm) x <- sweep(x, 2, rm) retval$colSDs <- sx <- apply(x, 2, sd, na.rm = na.rm) x <- sweep(x, 2, sx, "/") } > > I am finding it tricky to reproduce their results using > the z value above. What are you doing to reproduce the values? Best, Jim > > > Best, > > Tom > > _______________________________________________ > 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 Douglas Lab University of Michigan Department of Human Genetics 5912 Buhl 1241 E. Catherine St. Ann Arbor MI 48109-5618 734-615-7826