[BioC] How to display or output expression data with non-unique feature labels?

[Kocherginsky, Masha [BSD] - HSD]

Hello,

I'm learning (slowly) the way eSet and ExpressionSet classes work.  What
I want to do is probably quite simple, but I can't figure out the
following: how do I either display (onscreen) or write into a file the
expression levels of an ExpressionSet object AND include some or all
featureData?  For example, in the ExpressionSet generated below I have
g1-g5 replicated 4 times, and pos1-pos2 is replicated 10 times:

set.seed(31415)
exprs=data.frame(matrix(rnorm(100),nrow=20, ncol=5))
colnames(exprs)=letters[1:5]
pData=data.frame(matrix(rbinom(15,1,.5), nrow=5, byrow=T))
rownames(pData)=letters[1:5]
colnames(pData)=c("sex","agegrp","location")
phenoData=new("AnnotatedDataFrame", data=pData, 
  varMetadata=c("Gender","Age Group", "Location"))

fNames=rep(c("g1","g2","g3","g4","g5"),4)
fLoc=sort(rep(c("pos1","pos2"),10))
fData=data.frame(name=fNames, location=fLoc)
fDatalbl=data.frame(labelDescription=c("Name of Gene", "Location of

  Gene"), row.names=colnames(fData))
featureData=new("AnnotatedDataFrame", data=fData, varMetadata=fDatalbl)
data=new("ExpressionSet", exprs=exprs, phenoData=phenoData, 
  featureData=featureData)

> data
ExpressionSet (storageMode: lockedEnvironment)
assayData: 20 features, 5 samples 
  element names: exprs 
phenoData
  rowNames: a, b, ..., e (5 total)
  varLabels and varMetadata:
    sex: NA
    agegrp: NA
    location: NA
featureData
  rowNames: 1, 2, ..., 20 (20 total)
  varLabels and varMetadata:
    name: Name of Gene
    location: Location of       
      Gene
experimentData: use 'experimentData(object)'
Annotation character(0)


I'd like to get something like this using some accessor function (is
there one?):

  fNames fLoc        a        b        c        d        e
1     g1 pos1  1.64701  0.87221 -2.19476 -0.46615  1.01645
2     g2 pos1 -1.11199  1.05936  1.28965 -0.61097 -0.41773
3     g3 pos1 -1.54855  0.48339 -0.46200  1.17314 -0.09009
4     g4 pos1 -0.74838 -1.46186  0.35942 -0.87757 -1.33541
5     g5 pos1  1.52641 -0.39533  0.07781  1.26703  0.71262
6     g1 pos1 -1.13793  0.36251  0.45685  0.19561  1.16690

The data set I'm working with comes from a custom array with 3
replicates for each gene, and thus the "feature" names are not unique.
Am I setting up the ExpressionData object correctly? Is there a better
way than to incorporate non-unique gene names in exprs than to use gene
names via featureData? 

Thanks for any advice!
Masha
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Masha Kocherginsky, Ph.D.
Research Associate (Assistant Professor)
Department of Health Studies
University of Chicago
5841 S. Maryland Ave.
Chicago, IL  60637


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