[BioC] Heatmap function

Marcus marcusb at biotech.kth.se
Wed Oct 29 18:01:31 MET 2003

Hello. I am trying to get a visualization of my data with the help of the 
heatmap function that you have written. And I have some questions. I would 
really help me alot if someone would answer them.

I have a micorarray experiment consisting of 18 hybridizations where I have 
taken the M-values of a subset of the genes most likely to be 
differentially expressed and put them into a matrix (The dimension is 
18x3920). It is 3920 genes. It is on this matrix I have tried to apply the 
heatmapfunction. But I get the error message

Error in hclustfun(distfun(x)) : NA/NaN/Inf in foreign function call (arg 11)

I guess this is due to the fact that I do not have a value for each gene on 
each chip in the subset. Due to experimental errors some spots are only 
available on 2 of the 18 chips.
But I tried this bye making a testmatrix with dimension 5x4. The only time 
I got the same error message was if an entire row or an entire column 
contained only NA:s. But otherwise it worked. I have no row or column in my 
matrix that entirely consists of NA:s.
So I wonder if someone now of any limitations that are not in the helpfile.

Does anyone know of anywhere where one could read about how to use the 
heatmap function of other functions in the mva package. Because I do not 
really understand how to change for example the distfun argument by just 
reading the helpfile. I guess the distfun = dist is either single, average 
or complete linkage for the hclust used in the heatmap but how do one write 
to change the distfun argument? What does the function dist mean?

Best regards

/ M

Marcus Gry Björklund

Royal Institute of Technology
AlbaNova University Center
Stockholm Center for Physics, Astronomy and Biotechnology
Department of Molecular Biotechnology
106 91 Stockholm, Sweden

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