[BioC] Bug in featureNames() in R-2.5.0 / BioC 2.0?

[Groot, Philip de]

Hello list,
 
While checking my scripts against the new R/BioC versions, I encountered the following unexpected behaviour. Please consider the following peace of code:
 
library(simpleaffy)
x <- ReadAffy()
 
> x
AffyBatch object
size of arrays=1002x1002 features (14 kb)
cdf=Mouse430_2 (45101 affyids)
number of samples=6
number of genes=1004004
annotation=mouse4302
notes=

> featureNames(x)[1:5]
[1] "1" "2" "3" "4" "5"

> geneNames(x)[1:5]
[1] "1415670_at"   "1415671_at"   "1415672_at"   "1415673_at"   "1415674_a_at"

ADDITIONALLY: when I do the following, the output is correct:
 
x.norm <- rma(x)
 
> featureNames(x.norm)[1:5]
[1] "1415670_at"   "1415671_at"   "1415672_at"   "1415673_at"   "1415674_a_at"
> geneNames(x.norm)[1:5]
[1] "1415670_at"   "1415671_at"   "1415672_at"   "1415673_at"   "1415674_a_at"
Warning message:
'geneNames' is deprecated.
Use 'featureNames' instead.
See help("Deprecated")

 
Because of the "deprecated" message, I changed all geneNames() commands in featureNames() commands and hence found this inconsistency. I guess that my assumption is valid that the commands featureNames and geneNames should always obtain exactly the same results, is it not?
If not, please explain!
 
R/BioC is compiled and runnung on the following linux distribution:
SUSE LINUX Enterprise Server 9 (x86_64)
VERSION = 9
PATCHLEVEL = 3

The gcc version used is:
gcc (GCC) 3.3.3 (SuSE Linux)
Copyright (C) 2003 Free Software Foundation, Inc.
This is free software; see the source for copying conditions.  There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.

Regards,
 
Dr. Philip de Groot
Wageningen University