[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
Phone (office): +46 8 553 783 39
Fax: + 46 8 553 784 81
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