Thanks for the reply, I abbreviated the code to make my question clear. I am actually combining only certain rows and averaging the intensities based on certain criterion. A variation of your suggestion: " Or perhaps you want i to be a vector, either of integer values to indicate which rows to include, or a logical vector of length equal to the number of rows in RG$R, and then do (just once, not in a loop)" might suffice, I'll think about it. But...there is a significant difference in my case (ca. 10 mins vs. 30 second) between writing to a RGList and matrix, respectively. There is no reason for a copy of the RGList to be made (if that is what happens). Anyway, I am just puzzled why RGList is so slow. Thanks, -A -----Original Message----- From: Martin Morgan [mailto:mtmorgan@fhcrc.org] Sent: Thursday, February 05, 2009 1:39 PM To: Skewes,Aaron Cc: bioconductor at stat.math.ethz.ch Subject: Re: [BioC] RGList class is really slow, why? "Skewes,Aaron" <askewes at="" mdanderson.org=""> writes: > I am using RGList class, and desire to transform intensity values (R,Rb,G,Gb) and overwrite them into RGList object. If I do it row- wise: > > RG$R[i,]<-(R+RG2$R[i,])/(2) This probably copies the entire RG list, rather than just modifying the ith row of the R element of the RG list. This is necessary becasue R has 'copy on change' semantics, R makes a copy of an ojbect (in this case RG) when a component of it (in this case RG$R) is changed. Not sure what R or RG2 are, but what you might be aiming for is just RG$R <- R + RG$R / 2 this extracts the RG$R matrix, divides every element by two (which I guess you're doing but in a loop, with an index 'i') and then adds the content of whatever 'R' is. Or perhaps you want i to be a vector, either of integer values to indicate which rows to include, or a logical vector of length equal to the number of rows in RG$R, and then do (just once, not in a loop) RG$R[i,] <- R + RG$R[i,] / 2 There's still a copy possible (R can be clever and not make a copy if there are no other references to RG) but either way it should be so fast that speed isn't important. Hope that helps, Martin > The overwriting is really SLOWWWWWW. On the other hand, If I create a dummy matrix: > > QR=matrix(nrow=dim(RG)[1], ncol=dim(RG)[2]) > > And write the values to it: > > QR[i,]<-(R+RG2 $R[i,])/(2) > > It is relatively fast (of course I can do it this way, then simply RG$R <-QR, which is ok) > > But I'd really like to know why writing to a matrix is so much faster than RGList? Is RGList making a copy each time or something? > > > -Aaron > > > > [[alternative HTML version deleted]] > > _______________________________________________ > 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 -- Martin Morgan Computational Biology / Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: Arnold Building M2 B169 Phone: (206) 667-2793