[BioC] coerce matrix to aafTable
James W. MacDonald
jmacdon at med.umich.edu
Thu Nov 29 15:01:04 CET 2007
Hi Georg,
Georg Otto wrote:
> Hi,
>
> 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(probeids=rownames(matrix),
> "colname1"=matrix[,1],
> "colname2"=matrix[,2],
> "colname3"=matrix[,3],
> "colname4"=matrix[,4])
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.
Best,
Jim
>
> 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?
>
> Best,
>
> Georg
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
--
James W. MacDonald, M.S.
Biostatistician
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109
734-647-5623
More information about the Bioconductor
mailing list