[BioC] missing probe_id in ath1121501.db
Stefan Bleuler
stefan at nebion.com
Mon Feb 13 09:23:26 CET 2012
Hi,
I am working with the Bioconductor annotation package for the
Arabidopsis thaliana GeneChip ATH1 and have found a strange difference
between version 2.7 and versions 2.8 or 2.9.
In 2.7:
source("http://bioconductor.org/biocLite.R")
biocLite("ath1121501.db")
library("ath1121501.db")
length(as.list(toggleProbes(ath1121501ACCNUM,"all")))
produces the following output:
[1] 22810
In 2.8 or 2.9 the same code produces the following output:
[1] 22809
Comparing the lists of probe_ids shows that the probe_id 245651_s_at is
present in 2.7 and not present in 2.8 or 2.9. I know that the
annotations for a given probe_id can change with updates but why would a
probe_id be removed? This probe_id is still present in the latest
annotation files provided by Affymetrix.
Thanks for any idea.
Stefan Bleuler
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