Hi all,

I have a problem that concerns the use of annotation packages, here in an
example for a custom-made AGILENT microarray for Arabidopsis (but I think
it also concerns the org.At.tair.db package). I don't quite understand how
this issue arises, so sorry for the vague title (my guess is that it
concerns AnnotationDbi package version 1.18.1).

The issue is: if I query a GO-ID from my AGILENTv2GO2ALLPROBES bimap, I get
a very different result using a newer BioC version when compared to the
result using an older BioC version. Please note here that the annotation
package itself is the same in both versions used!

Here is the output from a query in the NEW version:


> library(AGILENTv2.db)

> genes <- get("GO:0006351", AGILENTv2GO2ALLPROBES)

> length(unique(genes))

[1] 1825

#### ok, so that would be 1825 unique genes/probes obtained from the query

> sessionInfo()

R version 2.15.0 (2012-03-30)

Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)


locale:

[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8


attached base packages:

[1] stats     graphics  grDevices utils     datasets  methods   base


other attached packages:

[1] AGILENTv2.db_2.6.4   org.At.tair.db_2.7.1 RSQLite_0.11.1
DBI_0.2-5            AnnotationDbi_1.18.1

[6] Biobase_2.16.0       BiocGenerics_0.2.0


loaded via a namespace (and not attached):

[1] IRanges_1.14.3 stats4_2.15.0

------------------------------------------
Now please compare this with the output from the OLD version.

> library(AGILENTv2.db)
> genes <- get("GO:0006351", AGILENTv2GO2ALLPROBES)
> length(unique(genes))
[1] 2122
#### here, there are 2122 unique genes/probes obtained, so many more than
the 1825 above, even though the AGILENTv2.db used was the same (version
2.6.4)
> sessionInfo()
R version 2.14.0 (2011-10-31)
Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)

locale:
[1] en_IE.UTF-8/en_IE.UTF-8/en_IE.UTF-8/C/en_IE.UTF-8/en_IE.UTF-8

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

other attached packages:
[1] AGILENTv2.db_2.6.4    org.At.tair.db_2.6.4  RSQLite_0.11.1
DBI_0.2-5             AnnotationDbi_1.16.10
[6] Biobase_2.14.0

loaded via a namespace (and not attached):
[1] IRanges_1.12.5

-------------------------

Any suggestions? I am not sure in which package the problem is, because the
annotation package should be identical. I think the same problem occurs in
the org.At.tair.db package, however, I have also different versions of the
annotation package installed on the different computers...

Thanks for any help,

Sam

-- 
----------------------------------------------------
Samuel Wuest
Institute of Evolutionary Biology and Environmental Studies
University of Zurich
Winterthurerstrasse 190
8057 Zurich, Switzerland
phone: +41 44 635 44 99
email: wuests@tcd.ie
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