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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Biostatistician
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University of Michigan
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