[BioC] Simpleaffy error : No methods found in "Biobase" for requests: geneNames

[Thornton, Matthew]

Hello,

I am trying to use simpleaffy to generate some QC information. When I load simpleaffy I am getting this error:

Warning messages:
1: found methods to import for function ‘as.list’ but not the generic itself
2: found methods to import for function ‘eapply’ but not the generic itself
>

Also if I proceed with the processing, following the exact procedure in "QC and Affymetrix data", by Wilson et. al., (except substituting my data and an alternative covdesc file) I get no output with ampli.eset <- call.exprs(ampli.data,"mas5"). Perhaps they are related?

here is the entire output.

R version 2.15.1 (2012-06-22) -- "Roasted Marshmallows"
Copyright (C) 2012 The R Foundation for Statistical Computing
ISBN 3-900051-07-0
Platform: x86_64-pc-linux-gnu (64-bit)

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Type 'license()' or 'licence()' for distribution details.

  Natural language support but running in an English locale

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

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> library(simpleaffy)
Loading required package: BiocGenerics

Attaching package: ‘BiocGenerics’

The following object(s) are masked from ‘package:stats’:

    xtabs

The following object(s) are masked from ‘package:base’:

    anyDuplicated, cbind, colnames, duplicated, eval, Filter, Find,
    get, intersect, lapply, Map, mapply, mget, order, paste, pmax,
    pmax.int, pmin, pmin.int, Position, rbind, Reduce, rep.int,
    rownames, sapply, setdiff, table, tapply, union, unique

Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: affy
Loading required package: genefilter
Loading required package: gcrma
No methods found in "Biobase" for requests: geneNames
Warning messages:
1: found methods to import for function ‘as.list’ but not the generic itself
2: found methods to import for function ‘eapply’ but not the generic itself
>
> getwd()
[1] "/home/gserver/GSE4182/test"
> ampli.data <- read.affy("covdesc")
> ampli.data
Loading required package: AnnotationDbi


AffyBatch object
size of arrays=1164x1164 features (18 kb)
cdf=HG-U133_Plus_2 (54675 affyids)
number of samples=2
number of genes=54675
annotation=hgu133plus2
notes=
>
> ampli.eset <- call.exprs(ampli.data, "mas5")
> ampli.eset
ExpressionSet (storageMode: lockedEnvironment)
assayData: 54675 features, 2 samples
  element names: exprs
protocolData: none
phenoData
  sampleNames: GSM94597.CEL GSM94598.CEL
  varLabels: sample SampleName Group
  varMetadata: labelDescription
featureData: none
experimentData: use 'experimentData(object)'
Annotation: hgu133plus2
> names(ampli.eset at description@preprocessing)
Error: no slot of name "description" for this object of class "ExpressionSet"
> names(ampli.eset at preprocessing)
Error: no slot of name "preprocessing" for this object of class "ExpressionSet"
> ampli.eset at preprocessing@preprocessing$sfs
Error: no slot of name "preprocessing" for this object of class "ExpressionSet"
>

Also if I proceed with the processing, following the exact procedure in "QC and Affymetrix data", by Wilson et. al., (except substituting my data and an alternative covdesc file) I get no output with ampli.eset <- call.exprs(ampli.data,"mas5").

Any advice on how to proceed would be greatly appreciated!

Thanks!

Sincerely,

Matt