[BioC] RMA warning message about missing se.exprs

[Martin Morgan]

Hi --

The version of affy you're using creates an 'se.exprs' slot with, I
think, a zero-dimension matrix. Biobase ExpressionSet has become more
picky about what se.exprs should look like, and in particular is
should have the same number of features and samples as exprs. So the
warning says that ExpressionSet took a particular action -- removed
the 'empty' se.exprs -- rather than create an invalid instance. The
warning about varLabels is similar, i.e., ExpressionSet doesn't know
what to do with the information.

The current version of Biobase and affy are back to thinking the same
about their data representation, and in fact rma produces an
ExpressionSet (despite what the documents say!):

> library(affy)
> example(rma)

rma> data(affybatch.example)

rma> eset <- rma(affybatch.example)
Background correcting
Normalizing
Calculating Expression

> eset
ExpressionSet (storageMode: lockedEnvironment)
assayData: 150 features, 3 samples 
  element names: exprs 
phenoData
  sampleNames: 20A, 20B, 10A
  varLabels and varMetadata:
    sample: arbitrary numbering
featureData
  featureNames: A28102_at, AB000114_at, ..., HG2188-HT2258_at (150 total)
  varLabels and varMetadata: none
experimentData: use 'experimentData(object)'
Annotation [1] ""

> sessionInfo()
R version 2.5.0 Patched (2007-04-24 r41305) 
x86_64-unknown-linux-gnu 

locale:
LC_CTYPE=en_US;LC_NUMERIC=C;LC_TIME=en_US;LC_COLLATE=en_US;LC_MONETARY=en_US;LC_MESSAGES=en_US;LC_PAPER=en_US;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US;LC_IDENTIFICATION=C

attached base packages:
[1] "tools"     "stats"     "graphics"  "grDevices" "utils"     "datasets" 
[7] "methods"   "base"     

other attached packages:
    affy   affyio  Biobase 
"1.14.0"  "1.4.0" "1.14.0" 

caiwei at mdanderson.org writes:

> Dear all,
>
> I am running RMA and MAS5 on some U133_Pluss_2 array  and get  this warning
> message :
>
>> x.rma <- as(rma(ab), "ExpressionSet")
> Warning messages:
> 1: missing or mis-shaped 'se.exprs' in original object; creating
> ExpressionSet without se.exprs in: asMethod(object)
> 2: contents of varLabels ignored
>
>> x.mas <- as(x.mas, "ExpressionSet")
> Warning messages:
> 1: missing or mis-shaped 'se.exprs' in original object; creating
> ExpressionSet without se.exprs in: asMethod(object)
> 2: contents of varLabels ignored
>
> I used these code lines:
>
> fnames <- paste(as.character(pData(pd)$ArrayName), "CEL", sep=".")
> ab <- read.affybatch(filenames=fnames, phenoData=pd, description=miame)
>
> x.mas <- as(x.mas, "ExpressionSet")
> x.rma <- as(rma(ab), "ExpressionSet")
> Background correcting
> Normalizing
> Calculating Expression
>
>
> R version 2.4.1 (2006-12-18)
> i686-pc-linux-gnu
>
> other attached packages:
>  hgu133plus2cdf  ClassDiscovery         cluster ClassComparison
> PreProcess
>        "1.14.0"           "1.3"        "1.11.4"           "1.3"
> "1.3"
>       oompaBase          xtable      colorspace     geneplotter
> annotate
>           "1.3"         "1.4-3"          "0.95"        "1.12.0"
> "1.12.1"
>      simpleaffy      genefilter        survival            affy
> affyio
>         "2.4.2"        "1.12.0"          "2.30"        "1.12.2"
> "1.2.0"
>         Biobase
>        "1.12.2"
>
>
> Highly appreciate any comments!
>
> Caimiao Wei
>
> UT M.D.Anderson Cancer Center
> 1515 Holcombe Blvd, Unit 237
> Houston, TX 77030-4009
>
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-- 
Martin Morgan
Bioconductor / Computational Biology
http://bioconductor.org