On Mon, 12 Feb 2007, andy1983 wrote: > > I would like to compare every column in my matrix with every other column and > get the r-squared. > > I tried using the following formula and looping through every column: >> summary(lm(matrix[,x]~matrix[,y]))$r.squared > If I have 10,000 columns, the loops (10,000 * 10,000) take forever even if > there is no formula inside. > > Then, I attempted to vectorize my code: >> cor(matrix)^2 > With 10,000 columns, this works great. With 30,000, R tells me it cannot > allocate vector of that length even if the memory limit is set to 4 GBs.
30000^2 doubles * 8 Bytes/double > 6.5 GBs. And that's just to store the result; you will need some space to work in, too. > > Is there anything else I can do to resolve this issue? > > Thanks. > -- > View this message in context: > http://www.nabble.com/processing-a-large-matrix-tf3216447.html#a8932591 > Sent from the R help mailing list archive at Nabble.com. > > ______________________________________________ > R-help@stat.math.ethz.ch mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide http://www.R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code. > Charles C. Berry (858) 534-2098 Dept of Family/Preventive Medicine E mailto:[EMAIL PROTECTED] UC San Diego http://biostat.ucsd.edu/~cberry/ La Jolla, San Diego 92093-0901 ______________________________________________ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.