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Groot, Philip de
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630
@groot-philip-de-1307
Last seen 10.1 years ago
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