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

[Freudenberg, Johannes (NIH/NIEHS) [E]]

Hi Jiang,

It sounds like you have NAs in your ID list.  Please check if 

> any(is.na(x$ID))

is TRUE.  You could also the following as an alternative way to get the Entrez IDs:

> x$ENTREZ <- toTable(mgu74av2ENTREZID)[match(x$ID, toTable(mgu74av2ENTREZID)[, 1]), 2]


--Johannes


-----Original Message-----
From: Jing Huang [mailto:huangji at ohsu.edu] 
Sent: Wednesday, August 24, 2011 11:49 AM
To: 'bioconductor at r-project.org'
Subject: [BioC] question on library(mgu74av2.db) for SPIA package application

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

I have used the same set of scripts for other annotation packages and have not had any problem.

Many many thanks

Jing

Oregon

	[[alternative HTML version deleted]]