In the old limma, one could subset a MAlist or RGlist (let's say RGnorm is a MAlist) by entering: RGnorm[,1:3] for the first three columns for example In the version, I'm using now (v1.8.1) this no longer works. > RGnorm[,1] Error in object$targets[j, , drop = FALSE] : incorrect number of dimensions Can someone help me with this. I'm running R v2.0.0 _ platform powerpc-apple-darwin6.8 arch powerpc os darwin6.8 system powerpc, darwin6.8 status major 2 minor 0.0 year 2004 month 10 day 04 language R Matt McCall

> Date: Tue, 14 Dec 2004 13:42:48 -0500 > From: Matt McCall <mmccall@mail.nih.gov> > Subject: [BioC] limma object column subsetting > To: bioconductor@stat.math.ethz.ch > > In the old limma, one could subset a MAlist or RGlist (let's say RGnorm > is a MAlist) by entering: > RGnorm[,1:3] for the first three columns for example > In the version, I'm using now (v1.8.1) this no longer works. It does still work as far as I can see. > > RGnorm[,1] > Error in object$targets[j, , drop = FALSE] : > incorrect number of dimensions > > Can someone help me with this. I'm running R v2.0.0 You don't make it clear what classs of object your RGnorm is. I am assuming it is an RGList or an MAlist. The problem seems to be that the 'targets' component of your object is a simple vector rather than a data frame as it is expected to be. How did you create the RGnorm and, in particular, how did you set the targets component? The only limma function which creats an RGList or MAList with the targets component set automatically is read.maimages(), and in that the case the 'targets' should be subsettable correctly. However you created RGnorm, you should be able to fix the above problem by RGnorm$targets <- as.data.frame(RGnorm$targets) or by RGnorm$targets <- NULL Gordon > _ > platform powerpc-apple-darwin6.8 > arch powerpc > os darwin6.8 > system powerpc, darwin6.8 > status > major 2 > minor 0.0 > year 2004 > month 10 > day 04 > language R > > Matt McCall