[BioC] question on library(mgu74av2.db) for SPIA package application

[James W. MacDonald]

Hi Jing,

On 8/24/2011 11:48 AM, Jing Huang wrote:
> Dear All members,
>
> I am using the library(mgu74av2.db), which is Affymetrix Murine Genome U74v2 annotation data (chip mgu74av2). I have an error message that I don’t understand. Could somebody advice me?
>
> Here is the R:
>
> library(SPIA)
> x=topTable(fit,coef="WThypo",n=1003)
> names(x)
>
> names(x)
> [1] "ID"                    "Gene.title"            "Gene.symbol"
>   [4] "Gene.ID"               "UniGene.title"         "UniGene.symbol"
>   [7] "UniGene.ID"            "Nucleotide.Title"      "GI"
> [10] "GenBank.Accession"     "Platform_CLONEID"      "Platform_ORF"
> [13] "Platform_SPOTID"       "Chromosome.location"   "Chromosome.annotation"
> [16] "GO.Function"           "GO.Process"            "GO.Component"
> [19] "GO.Function.1"         "GO.Process.1"          "GO.Component.1"
> [22] "logFC"                 "AveExpr"               "t"
> [25] "P.Value"               "adj.P.Val"             "B"
>
> library(mgu74av2.db)
> mgu74av2()
> y=mgu74av2ENTREZID
> x$ENTREZ=unlist(as.list(y[x$ID]))
>
> Error in as.list(y[x$ID]) :
>    error in evaluating the argument 'x' in selecting a method for function 'as.list': Error in .checkKeysAreWellFormed(keys) :
>    keys must be supplied in a character vector with no NAs

The above error is saying that your x$ID vector contains NA values. You 
need to subset out the NAs first.

Best,

Jim


>
> I have used the same set of scripts for other annotation packages and have not had any problem.
>
> Many many thanks
>
> Jing
>
> Oregon
>
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>
>
>
>
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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.
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