[BioC] coerce matrix to aafTable
James W. MacDonald
jmacdon at med.umich.edu
Thu Nov 29 15:01:04 CET 2007
Georg Otto wrote:
> I have an R/bioconductor problem, that seemed to be quite simple to me
> at the first glance, but turned out to be tricky, either because I do
> not have reached the necessary level of R-savvyness yet, or because I
> miss something obvious.
> Here is the problem: I want to transform a matrix of expression
> values (where rows are genes and columns are hybridizations) into an
> aafTable (from package annaffy). The probe IDs should be taken from
> the row names of the matrix and the column names should be taken from
> the column names of the matrix. No problem to do this by hand:
table <- aafTable(items = as.data.frame(matrix))
This can be rather computationally expensive if the matrices are large,
but it is probably the simplest solution.
> I would like to do that programatically for many different matrices
> which differ both in the number of columns and in the column names,
> maybe by using a small function. However I was not successful to
> contrive such a thing. Maybe somebody out there could give me a hint?
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James W. MacDonald, M.S.
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
Ann Arbor MI 48109
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