That indeed solved the problem. > annotation(esetPROC) <- "hgug4112a" # Very important. Must remove that .db from the name of the annotation package. > esetGSEA <- nsFilter(esetPROC, require.entrez=TRUE, require.GOBP=TRUE, remove.dupEntrez=TRUE, var.func=IQR, var.cutoff=0.3) # cutoff at about the mean value xof my irqs Thank you. I don't know how many weeks would have this taken without the help from this list! Massimo On Fri, Oct 30, 2009 at 5:26 PM, Robert Gentleman <rgentlem at="" gmail.com=""> wrote: > Hi > > Robert Gentleman > > On Oct 30, 2009, at 7:11 AM, Massimo Pinto <pintarello at="" gmail.com=""> wrote: > >> Greetings all, >> >> I have finally come across to genefilter's nsFIlter(); it looks like >> it's going to do quite a lot for me in just one call. ?I called it as >> follows: >> >>> esetGSEA <- nsFilter(esetPROC, require.entrez=TRUE, require.GOBP=TRUE, >>> remove.dupEntrez=TRUE, var.func=IQR, var.cutoff=0.5) >> >> Error in do.call(paste(chip, "_dbconn", sep = ""), list()) : >> ?could not find function "hgug4112a.db_dbconn" >> >>> annotation(esetPROC) >> >> [1] "hgug4112a.db" >> > > This is probably part of the problem > Drop the .db suffix it is not part of the annotation. > You should Use "hgug4112a" > > >> here's some info on my session: >> >>> sessionInfo() >> >> R version 2.10.0 (2009-10-26) >> x86_64-apple-darwin9.8.0 >> >> locale: >> [1] C >> >> attached base packages: >> [1] grid ? ? ?tcltk ? ? stats ? ? graphics ?grDevices utils >> datasets ?methods ? base >> >> other attached packages: >> [1] affy_1.24.0 ? ? ? ? ? ? gplots_2.7.3 ? ? ? ? ? ?caTools_1.10 >> ? ? bitops_1.0-4.1 ? ? ? ? ?gdata_2.6.1 ? ? ? ? ? ? gtools_2.6.1 >> [7] hgug4112a.db_2.3.5 ? ? ?org.Hs.eg.db_2.3.6 ? ? ?RSQLite_0.7-3 >> ? ? DBI_0.2-4 ? ? ? ? ? ? ? Agi4x44PreProcess_1.5.1 >> genefilter_1.28.0 >> [13] annotate_1.24.0 ? ? ? ? AnnotationDbi_1.7.20 ? ?limma_3.2.1 >> ? ? Biobase_2.6.0 >> >> loaded via a namespace (and not attached): >> [1] affyio_1.13.5 ? ? ? ?preprocessCore_1.7.9 splines_2.10.0 >> survival_2.35-7 ? ? ?tools_2.10.0 ? ? ? ? xtable_1.5-5 >> >> Thanks a lot, >> Yours >> Massimo >> >> Massimo Pinto >> Post Doctoral Research Fellow >> Enrico Fermi Centre and Italian Public Health Research Institute (ISS), >> Rome >> http://claimid.com/massimopinto >> >> _______________________________________________ >> 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 >> >