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)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
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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Type 'q()' to quit R.

> 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@description@preprocessing)
Error: no slot of name "description" for this object of class "ExpressionSet"
> names(ampli.eset@preprocessing)
Error: no slot of name "preprocessing" for this object of class "ExpressionSet"
> ampli.eset@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


Matthew E. Thornton

Laboratory Technician III
Broad Center for Stem Cell and Regenerative Medicine

University of Southern California
1501 San Pablo St. ZNI
Los Angeles, CA 90089-2821

ph.:323-442-1688
fx.:323-442-4040
matthew.thornton@med.usc.edu

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