Hi bioconductor users, I am learning bioconductor by following the on-line short courses. This was what happened when I tried some code in "Differential expression" >library(annotate) >library(hgu95av2) >chr <- getCHR(geneNames(ALLSub), "hgu95av2") Error: couldn't find function "getCHR" >chr <- mget(geneNames(ALLSub), env=hgu95av2CHR) >ll <- getLL(geneNames(ALLSub), "hgu95av2") >ll.chr <- tapply(chr, ll, unique) Error in unique.default(X[[as.integer(1)]], ...) : unique() applies only to vectors >ll.chr <- tapply(unlist(chr), ll, unique) Error in tapply(unlist(chr), ll, unique) : arguments must have same length >length(chr) [1] 2400 >length(ll) [1] 2400 >length(unlist(chr)) [1] 2408 > Is this caused by a bug in "unlist" like an unaccessable link in google search said, or I have done something wrong here? how can I solve this problem? Thanks. Irene

On Mon, Jul 05, 2004 at 11:49:07AM -0700, Irene Li wrote: > Hi bioconductor users, > > I am learning bioconductor by following the on-line short courses. This was > what happened when I tried some code in "Differential expression" > >library(annotate) > >library(hgu95av2) > >chr <- getCHR(geneNames(ALLSub), "hgu95av2") > Error: couldn't find function "getCHR" > >chr <- mget(geneNames(ALLSub), env=hgu95av2CHR) > >ll <- getLL(geneNames(ALLSub), "hgu95av2") > >ll.chr <- tapply(chr, ll, unique) > Error in unique.default(X[[as.integer(1)]], ...) : > unique() applies only to vectors > >ll.chr <- tapply(unlist(chr), ll, unique) > Error in tapply(unlist(chr), ll, unique) : > arguments must have same length > >length(chr) > [1] 2400 > >length(ll) > [1] 2400 > >length(unlist(chr)) > [1] 2408 > > > > Is this caused by a bug in "unlist" like an unaccessable link in google > search said, or I have done something wrong here? how can I solve this > problem? No, it is not a bug in unlist. If you have multiple values in one (or more) of the list elements then the resulting *vector* is longer. For other hash tables (those that encode GO or PubMed relationships) the effect is much more dramatic. Now, you might think that all genes are annotated to only one chromosome - but that is in fact not true. It is pretty straightforward to identify those genes with multiple annotations - and you must then make some decision about what you want to do. Best, Robert ps: > l1 = list(a=1:3, b=4:7) > unlist(l1) a1 a2 a3 b1 b2 b3 b4 1 2 3 4 5 6 7 > length(l1) [1] 2 > > Thanks. > > Irene > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://www.stat.math.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 | +--------------------------------------------------------------------- ------+