[BioC] how to convert a AffyBatch into ExpressionSet object ?

[Min Wook Kim]

Dear all,
I tried to convert a object of AffyBatch into one of ExpressionSet.
but I couldn't get exactly same information between them, actually,
The data between original data and the modified data from gcrma was
compared.

The problem was that the assayData and fetureaData didn't match. Do I
have to make new object of AssayData and featuredata by using "new
command" ? are there any easy way ? e.g. some function to copy from
one to the other.

I did it like ;
> abatch
AffyBatch object
size of arrays=1002x1002 features (8 kb)
cdf=Mouse430_2 (45101 affyids)
number of samples=4
number of genes=45101
annotation=mouse4302
notes=
> tmp <- new ("ExpressionSet", phenoData = phenoData(abatch) , featureData = featureData(abatch), experimentData = experimentData(abatch), annotation = annotation(abatch),  assayData= assayData(abatch))


And what's difference between the following statement and above which
were different in assayData defined and exprs )

> tmp <- new ("ExpressionSet", phenoData = phenoData(abatch) , featureData = featureData(abatch), experimentData = experimentData(abatch), annotation = annotation(abatch),   exprs = exprs(abatch) )

-------------------------------------------
Finally, I want to make the same structure of the following two
objects except the value depending on the effect of gcrma. myRMA was
the output of gcrma. Maybe, my trying has a big misunderstanding of
them. if do it, please tell me it.


> myRMA
ExpressionSet (storageMode: lockedEnvironment)
assayData: 14707 features, 4 samples
  element names: exprs
phenoData
  sampleNames: HM1_24, HM1_25, Flt3_a, Flt3_b
  varLabels and varMetadata:
    sample: arbitrary numbering
    pheno1: arbitrary numbering
featureData
  rowNames: 1415670_at, 1415671_at, ..., AFFX-TransRecMur/X57349_3_at
(14707 total)
  varLabels and varMetadata: none
experimentData: use 'experimentData(object)'
Annotation [1] "mouse4302"
> tmp
ExpressionSet (storageMode: lockedEnvironment)
assayData: 1004004 features, 4 samples
  element names: exprs
phenoData
  sampleNames: HM1_24, HM1_25, Flt3_a, Flt3_b
  varLabels and varMetadata:
    sample: arbitrary numbering
    pheno1: arbitrary numbering
featureData
  featureNames: 1, 2, ..., 1004004 (1004004 total)
  varLabels and varMetadata: none
experimentData: use 'experimentData(object)'
Annotation [1] "mouse4302"
--------------------------------------------------------------------

And additionally, I haven't been able find the picture of description
about the hierarchy of classes ; especially Affybatch , EspressionSet
and eSet. If to exist, it would be so helpful.




> sessionInfo()
R version 2.5.1 (2007-06-27)
powerpc64-unknown-linux-gnu

locale:
LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=en_US.UTF-8;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C

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

other attached packages:
mouse4302cdf          vsn       marray    tkWidgets      GOstats     Category
    "1.16.0"      "2.2.0"     "1.14.0"     "1.14.0"      "2.2.6"      "2.2.3"
      Matrix         RBGL        graph     multtest      annaffy         KEGG
"0.999375-1"     "1.12.0"     "1.14.2"     "1.16.1"      "1.8.1"     "1.16.1"
          GO        limma affyQCReport  geneplotter      lattice     annotate
    "1.16.0"     "2.10.5"     "1.14.0"     "1.14.0"    "0.15-11"     "1.14.1"
RColorBrewer      affyPLM        gcrma  matchprobes     affydata       xtable
     "1.0-1"     "1.12.0"      "2.8.1"      "1.8.1"     "1.11.3"      "1.5-1"
  simpleaffy   genefilter     survival         affy       affyio      Biobase
   "2.10.31"     "1.14.1"       "2.32"     "1.14.2"      "1.4.1"     "1.14.1"
      DynDoc  widgetTools
    "1.14.0"     "1.12.0"