[BioC] an apparently strange case of 'Warning: number of items to replace is not a multiple of replacement length'
James W. MacDonald
jmacdon at med.umich.edu
Mon Oct 19 15:13:06 CEST 2009
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
>
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--
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
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