On Aug 28, 2011, at 1:20 PM, Paul Hammer wrote:
Dear folks,
I would like to compare two unequal matrices.
"Unequal " is hardly an adequate data description.
At the moment I realize
this with two for loop and an if function but that's definitely too
slow
:(...
Here is my code:
for (i in 1:length(all_expressed_genes[,1])) {
for (j in 1:length(kegg_gene_pVal[,1])) {
if (all_expressed_genes[j,1] == kegg_gene_pVal[i,1]) {
kegg_gene_pVal[j,4] = all_expressed_genes[i,6]
}
}
}
Are there any faster solutions for that easy code?
I'm trying to figure out what this is supposed to be doing. You are
making N^2 comparisons and transferring results from one vector of
length N to another vector of length N. Is this really what the (non-
existent) problem definition would have told us to do if you had
provided a problem definition? It appears there would be a great
possibility of overwriting earlier operations. And it appears to be
doing N^2-N unnecessary operations as well.
And why is R so
dramatically slow when using for, while or other loop functions?
Blaming the tool is generally a risky idea. Axes can be used
effectively or ineffectively. I'm guessing inadequate "operator"
training and/or confused problem specification.
*---------------------*
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and provide commented, minimal, self-contained, reproducible code.
*---------------------*
David Winsemius, MD
West Hartford, CT
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