Dear all, I'm getting an error message when trying to convert an old exprSet
object to the ExpressionSet class. "oncogene" is an exprSet object that I
first load.

> class(oncogene)
[1] "exprSet"
attr(,"package")
[1] "Biobase"

> slotNames(oncogene)
[1] "exprs"             "se.exprs"          "description"
[4] "annotation"        "notes"             "reporterInfo"
[7] "phenoData"         ".__classVersion__"

> newoncogene <- as(oncogene,"ExpressionSet")
Error in asMethod(object) :
  trying to get slot "description" from an object (class "exprSet") that is
not an S4 object

So the usual "as" conversion doesn't seem to work. Actually I'm not even
allowed to manually access any of the slots, so I can't even create the
ExpressionSet extracting each piece of information carefully.

> oncogene@annotation
Error: trying to get slot "annotation" from an object (class "exprSet") that
is not an S4 object

> head(oncogene@exprs)
Error: trying to get slot "exprs" from an object (class "exprSet") that is
not an S4 object
Error in head(oncogene@exprs) :
  error in evaluating the argument 'x' in selecting a method for function
'head'

> head(exprs(oncogene))
Error in function (classes, fdef, mtable)  :
  unable to find an inherited method for function "exprs", for signature
"exprSet"
Error in head(exprs(oncogene)) :
  error in evaluating the argument 'x' in selecting a method for function
'head'

I haven't found this problem posted anywhere. I know that exprSet has been
deprecated but the conversion method should still work right?
My session info is below, thanks in advance for any hints,

David

> sessionInfo()
R version 2.8.1 (2008-12-22)
i386-apple-darwin8.11.1

locale:
C

attached base packages:
[1] splines   tools     stats     graphics  grDevices utils     datasets
[8] methods   base

other attached packages:
 [1] convert_1.18.0       marray_1.20.0        MDA_1.0.1
 [4] Heatplus_1.12.0      mouse4302.db_2.2.5   hgu133a.db_2.2.5
 [7] hgu133plus2.db_2.2.5 RSQLite_0.7-1        DBI_0.2-4
[10] biomaRt_1.16.0       hopach_2.3.0         gaga_1.1.1
[13] coda_0.13-4          lattice_0.17-17      ada_2.0-1
[16] sma_0.5.15           randomForest_4.5-28  ClassDiscovery_2.5.0
[19] PreProcess_2.5.0     oompaBase_2.5.0      gplots_2.6.0
[22] gdata_2.4.2          gtools_2.5.0         limma_2.16.5
[25] MLInterfaces_1.22.0  cluster_1.11.11      annotate_1.20.1
[28] xtable_1.5-5         AnnotationDbi_1.4.2  rda_1.0
[31] rpart_3.1-42         genefilter_1.22.0    survival_2.34-1
[34] MASS_7.2-45          Biobase_2.2.2

loaded via a namespace (and not attached):
[1] RCurl_0.93-0 XML_1.99-0   grid_2.8.1

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