> Dear Users, > > I am following the example on Lab 5: Cluster analysis (June > 2003) with > my own data. > > I have filtered my expression set as shown on the example and I get > the following > > > sub <- genefilter(X,ffun) > > sum(sub) > [1] 1124 > > I save this subset of genes and then log transform it. But > when I type > the next command I get the following error: > > X <- X[sub,] > > X <- log2(X) > > RawDataSub <- Raw.Data[,sub] > Error in Raw.Data[, sub] : (subscript) logical subscript too long it looks like you are tyring to select columns not rows, RawDataSub <- Raw.Data[,sub] #subsets on columns try: RawDataSub <- Raw.Data[sub,] #subset on rows hth claire -------------------------------------------------------- This email is confidential and intended solely for the use o...{{dropped}}

On Tue, Nov 09, 2004 at 12:59:41PM +0100, kfbargad@lg.ehu.es wrote: > Dear Users, > > I am following the example on Lab 5: Cluster analysis (June 2003) with > my own data. > > I have filtered my expression set as shown on the example and I get > the following > > > sub <- genefilter(X,ffun) > > sum(sub) > [1] 1124 > > I save this subset of genes and then log transform it. But when I type > the next command I get the following error: > > X <- X[sub,] > > X <- log2(X) > > RawDataSub <- Raw.Data[,sub] > Error in Raw.Data[, sub] : (subscript) logical subscript too long > > Why do I get this error?? Perhaps because the dimensions of X and of Raw.Data are not the same? If you are not familiar with R you should spend some time with introductory material to learn about the language as that knowledge is essential for debugging. > Also, if I have stored the subset expression data as X, why is Raw.Data > [,sub] using [,sub] again? I don?t really understand this step, if > anyone could explain its purpose. > Because X and Raw.Data are not the same object. R basically has pass by value semantics and so (almost) everything is a copy. > I?m running R 1.9.1 on an XP computer > > Thanks a lot for your help > > David > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor -- +--------------------------------------------------------------------- ------+ | Robert Gentleman phone : (617) 632-5250 | | Associate Professor fax: (617) 632-2444 | | Department of Biostatistics office: M1B20 | | Harvard School of Public Health email: rgentlem@jimmy.harvard.edu | +--------------------------------------------------------------------- ------+