[R] heatmap.2: question regarding the "raw z-score"

[James W. MacDonald]

Hi Chrysanthi,

Chrysanthi A. wrote:
> Hi,
> 
> I am analysing gene expression data using the heatmap.2 function in R and I
> was wondering what is the formula of the "raw z-score" bar which shows the
> colors for each pixel.
> According to that post:
> https://mailman.stat.ethz.ch/pipermail/r-help/2006-September/113598.html, it
> is the
> 
> (actual value - mean of the group) / standard deviation.
> 
> But, mean of which group? Mean of the gene vector? And actual value of that
> gene on a sample?  I would be grateful if you could give me some more
> details about it or even if there is a book/manual that I could address
> to..

How about looking at the code?

     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, "/")
     }

So the z-score is calculated on either the row or column (or the default 
of "none").

I don't see how you can get something saying 'raw z-score'. I get either 
'Row Z-Score' or 'Column Z-Score'. So assuming you meant Row Z-Score, 
then the rows are centered and scaled by subtracting the mean of the row 
from every value and then dividing the resulting values by the standard 
deviation of the row.

Best,

Jim


> 
> Thanks a lot,
> 
> Chrysanthi.
> 
> *
> *
> 
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-- 
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