Hi Jim, hi Assa, thanks for drawing my attention to this bug. In the next few weeks, I will add some functionality to the functions which automatically set the arguments to FALSE if the corresponding mapping does not exist in the annotation package. But I am not sure if this will happen before the next release of BioConductor. Best, Holger -------- Original-Nachricht -------- > Datum: Thu, 26 Mar 2009 08:30:07 -0400 > Von: "James W. MacDonald" <jmacdon at="" med.umich.edu=""> > An: Assa Yeroslaviz <frymor at="" gmail.com=""> > CC: bioconductor at stat.math.ethz.ch > Betreff: Re: [BioC] Error message when working with sam > Hi Assa, > > Assa Yeroslaviz wrote: > > Hi, > > > > I'm trying to link my sig. genes with the web. by doing so I tried both > > sam2html and link.siggenes: > > > > sam2html(samresult, 20, "samresults_overview.html", > chipname="ath1121501") > > > > link.siggenes(samresult, 20, filename="samresults.html", addDataFrame = > > TRUE, title="SAM results - stress", > > entrez = FALSE, refseq = FALSE, symbol = TRUE, omim = FALSE, ug > = > > FALSE, > > fullname = TRUE, which.refseq = "NM", chipname="ath1121501", > > cdfname="ath1121501") > > > > I keep getting the error messagees: > > Error in get(mapName, envir = pkgEnv, inherits = FALSE) : > > variable "ath1121501ENTREZID" was not found > > That's because there are no mappings between this chip and Entrez Gene > IDs in the ath11215001.db package. You can see what mappings do exist by > loading the package and then using the ls() function: > > > library(ath1121501.db) > Loading required package: AnnotationDbi > Loading required package: DBI > > ls(2) > [1] "ath1121501" "ath1121501_dbconn" > "ath1121501_dbfile" > [4] "ath1121501_dbInfo" "ath1121501_dbschema" > "ath1121501ACCNUM" > [7] "ath1121501ARACYC" "ath1121501ARACYCENZYME" "ath1121501CHR" > > [10] "ath1121501CHRLENGTHS" "ath1121501CHRLOC" > "ath1121501CHRLOCEND" > [13] "ath1121501ENZYME" "ath1121501ENZYME2PROBE" > "ath1121501GENENAME" > [16] "ath1121501GO" "ath1121501GO2ALLPROBES" > "ath1121501GO2PROBE" > [19] "ath1121501MAPCOUNTS" "ath1121501ORGANISM" "ath1121501PATH" > > [22] "ath1121501PATH2PROBE" "ath1121501PMID" > "ath1121501PMID2PROBE" > [25] "ath1121501SYMBOL" > > > If you look at the help for the functions you are trying to use, you > will see that there is an 'entrez' argument that you can set to FALSE so > it won't try to do Entrez Gene mappings. Depending on what mappings do > exist in this annotation package, you may need to set other arguments to > FALSE as well. > > Best, > > Jim > > > > > > Error in mget(x, envir = getAnnMap(what, chip = data, load = load), > > ifnotfound = NA) : > > error in evaluating the argument 'envir' in selecting a method for > > function 'mget' > > > > so I was forced toturn them off. Is there a way of using this > information. > > I'm using R2.8.1 with Bioconductior 2.3. (I think) > > > > THX, > > > > Assa > > > > [[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 > > -- > James W. MacDonald, M.S. > Biostatistician > Douglas Lab > 5912 Buhl > 1241 E. Catherine St. > Ann Arbor MI 48109-5618 > 734-615-7826 > > _______________________________________________ > 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 --