Thanks! Ramsi On Thu, 2005-03-10 at 15:20, James W. MacDonald wrote: > Ramsi Haddad wrote: > > Dear List, > > > > I have been using the function htmlpage() from the annotate package. > > It used to be called ll.htmlpage(). It generates an html page with > > hotlinks to LocusLink. Now I click a link, the locuslink page tells me > > its closed and that I'll be redirected to Gene. I've looked at the code > > and it referred to a function getQueryLink(). this last function does > > not have an entry for Entrez Gene. Has anyone else dealt with this > > problem? Thanks for your assistance. > > The fix for this is relatively simple, but unfortunately will not be > propagated to the release version until April or so, when the new BioC > release occurs. > > A simple fix is to replace the function getQuery4LL() with this: > > getQuery4LL <- function (ids) > { > if (is.factor(ids)) { > options(warn = -1) > ids <- as.numeric(as.character(ids)) > options(warn = 0) > blanks <- is.na(ids) > } > if (is.character(ids)) { > options(warn = -1) > ids <- as.numeric(ids) > options(warn = 0) > blanks <- is.na(ids) > } > if (is.numeric(ids)) > blanks <- is.na(ids) > out <- vector() > for (i in seq(along = ids)) { > if (!blanks[i]) > out[i] <- > paste("http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gene&cmd=Ret rieve&dopt=Graphics&list_uids=", > > ids[i], sep = "") > else out[i] <- " " > } > return(out) > } > > HTH, > > Jim > > > > > > Ramsi > > >