Question: an apparently strange case of 'Warning: number of items to replace is not a multiple of replacement length'
0
gravatar for Massimo Pinto
10.1 years ago by
Massimo Pinto390
Massimo Pinto390 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 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
go hgug4112a • 6.2k views
ADD COMMENTlink modified 10.1 years ago by James W. MacDonald51k • written 10.1 years ago by Massimo Pinto390
Answer: an apparently strange case of 'Warning: number of items to replace is not a mult
0
gravatar for James W. MacDonald
10.1 years ago by
United States
James W. MacDonald51k 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
ADD COMMENTlink written 10.1 years ago by James W. MacDonald51k
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 >
ADD REPLYlink written 10.1 years ago by Massimo Pinto390
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 343 users visited in the last hour