That was indeed the case. Thank you, James. This has revealed a problem that refers, possibly, to pre-processing and which is now subject of a dedicated thread: https://stat.ethz.ch/pipermail/bioconductor/2009-October/030100.html Yours Massimo Massimo Pinto Post Doctoral Research Fellow Enrico Fermi Centre and Italian Public Health Research Institute (ISS), Rome http://claimid.com/massimopinto On Mon, Oct 19, 2009 at 3:13 PM, James W. MacDonald <jmacdon at="" med.umich.edu=""> wrote: > Hi Massimo, > > Massimo Pinto wrote: >> >> Greetings, >> >> I have encountered a series of warning messages when copying indices >> into a vector of integers. Specifically: >> >>> Geni_GO_0033554_CM3.ctr3 <- as.integer(unlist(geneIdsByCategory(hgOver.6, >>> "GO:0033554"), use.names = FALSE)) >> >> [1] 100133315 ? ? 10714 ? ? ?1112 ? ? 11198 ? ? ?1643 ? ? ?2237 >> 26057 ? ? 27113 ? ? ?4913 ? ? 50484 ? ? ?5429 ? ? 57697 ? ? ?5796 >> 5885 ? ? ?7516 ? ? ?8445 >> >>> myrows<- integer(length=length(Geni_GO_0033554_CM3.ctr3)) >> >> + for (i in 0:length(Geni_GO_0033554_CM3.ctr3)) { >> + myrows[i] <- which(Age_LNGSVsISS.topTable.2k[, >> "mappings.Sub.ENTREZID"] == Geni_GO_0033554_CM3.ctr3[i]) >> + } >> >> Warning messages: >> 1: In myrows[i] <- which(Age_LNGSVsISS.topTable.2k[, >> "mappings.Sub.ENTREZID"] == ?: >> ?number of items to replace is not a multiple of replacement length >> 2: In myrows[i] <- which(Age_LNGSVsISS.topTable.2k[, >> "mappings.Sub.ENTREZID"] == ?: >> ?number of items to replace is not a multiple of replacement length >> 3: In myrows[i] <- which(Age_LNGSVsISS.topTable.2k[, >> "mappings.Sub.ENTREZID"] == ?: >> ?number of items to replace is not a multiple of replacement length >> 4: In myrows[i] <- which(Age_LNGSVsISS.topTable.2k[, >> "mappings.Sub.ENTREZID"] == ?: >> ?number of items to replace is not a multiple of replacement length > > This is because at least 4 of the Entrez Gene IDs appear more than once in > the vector Age_LNGSVsISS.topTable.2k[,"mappings.Sub.ENTREZID"]. When you use > the which() function on a vector for which the equality is true more than > once you will get a vector: > >> which(rep(3,3) == 3) > [1] 1 2 3 > > And you cannot put a vector into a single position of another vector: > >> a <- 1:10 >> a[1] <- 1:3 > Warning message: > In a[1] <- 1:3 : > ?number of items to replace is not a multiple of replacement length > > Best, > > Jim > > >> >> I have looked into a former discussion on this list >> http://tolstoy.newcastle.edu.au/R/help/04/09/4534.html >> but could not find the reason for getting an error in my case. >> >> Apparently, I am not missing any item of those that I wish to copy; >> still, I am getting a warning and would prefer to clarify this matter. >> >> Thank you all in advance, >> Massimo >> >> sessionInfo follows: >> >>> sessionInfo() >> >> R version 2.9.1 (2009-06-26) >> i386-apple-darwin8.11.1 >> >> locale: >> C >> >> attached base packages: >> [1] stats ? ? graphics ?grDevices utils ? ? datasets ?methods ? base >> >> other attached packages: >> ?[1] GO.db_2.2.11 ? ? ? ?hgug4112a.db_2.2.11 limma_2.18.0 >> GOstats_2.10.0 ? ? ?RSQLite_0.7-1 ? ? ? DBI_0.2-4 >> graph_1.22.2 ? ? ? ?Category_2.10.0 >> ?[9] AnnotationDbi_1.6.0 Biobase_2.4.1 >> >> loaded via a namespace (and not attached): >> [1] GSEABase_1.6.0 ? ?RBGL_1.20.0 ? ? ? XML_2.3-0 >> annotate_1.22.0 ? genefilter_1.24.0 splines_2.9.1 ? ? survival_2.35-4 >> ?tools_2.9.1 ? ? ? xtable_1.5-5 >> >> >> 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 > > -- > James W. MacDonald, M.S. > Biostatistician > Douglas Lab > University of Michigan > Department of Human Genetics > 5912 Buhl > 1241 E. Catherine St. > Ann Arbor MI 48109-5618 > 734-615-7826 >