[Bioc-devel] Different behavior of get() between 2.9.0 and later versions`

Hi Luigi,

On 11/3/09 8:37 PM, Luigi Marchionni wrote:

here is Luigi. I am developing a package which heavily relies on
AnnotationDbi, annotate, and metadatata packages from bioconductor.
I noticed I weird behavior of the get() function for the  
mgug4122a.db()
package moving from 2.9.1 to later versions (2.10.0 and 2.11.0 the  
one I
am running).
Basically, an ID pointing to an 'NA' is not properly handled in the
newer versions, see below.
The same ID in one case returns 'NA', in the other case returns an  
error.
If also checked if this happened with other package (hgu133a.db)  
and the
behavior is different, for both an ID that was there and now is  
missing,
and an ID that was not there, and now is not there as well....
I give you the details below. Do you have any idea of what is going  
on?

Partial details...

When you call get() or otherwise retrieve a value from an annotation  
package object using a key, like a probe ID, there are three  
situations:

1. The probe ID is valid and maps to a value in the given object.
2. The probe ID is valid, but does not map to a value so NA is  
returned.
3. The probe ID is not valid, an error is raised.

So using a part of your example I see:

get("A_52_P71146", mgug4122aSYMBOL)

Error in .checkKeys(value, Lkeys(x), x at ifnotfound) :
 value for "A_52_P71146" not found

"A_52_P71146" %in% keys(mgug4122aSYMBOL)

[1] FALSE

I'll let someone else take a crack at why the key sets would have  
changed.

+ seth

sessionInfo()

R version 2.11.0 Under development (unstable) (--)
x86_64-unknown-linux-gnu

locale:
[1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=C              LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8       LC_NAME=C
[9] LC_ADDRESS=C               LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

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

other attached packages:
[1] mgug4122a.db_2.3.5  org.Mm.eg.db_2.3.6  RSQLite_0.7-3
[4] DBI_0.2-4           AnnotationDbi_1.9.0 Biobase_2.5.8

loaded via a namespace (and not attached):
[1] tools_2.11.0

Luigi

########################################################
###FOR R-2.9.1:
########################################################

sessionInfo()

R version 2.9.1 (2009-06-26)
i386-apple-darwin9.7.0

locale:
en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8

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

other attached packages:
[1] hgu133a.db_2.2.12 mgug4122a.db_2.2.11
[3] RSQLite_0.7-3 DBI_0.2-4
[5] AnnotationDbi_1.6.1 Biobase_2.4.1

get("A_52_P71146", mgug4122aSYMBOL)

[1] NA

get("201265_at", hgu133aSYMBOL)

[1] NA

get("200080_s_at", hgu133aSYMBOL)

[1] "H3F3A"

########################################################
###FOR R-2.10.0:
########################################################

sessionInfo()

R version 2.10.0 (2009-10-26)
i386-apple-darwin9.8.0

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

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

other attached packages:
[1] hgu133a.db_2.3.5 org.Hs.eg.db_2.3.6
[3] mgug4122a.db_2.3.5 org.Mm.eg.db_2.3.6
[5] RSQLite_0.7-3 DBI_0.2-4
[7] AnnotationDbi_1.8.0 Biobase_2.6.0

get("A_52_P71146", mgug4122aSYMBOL)

Error in .checkKeys(value, Lkeys(x), x at ifnotfound) :
value for "A_52_P71146" not found

get("201265_at", hgu133aSYMBOL)

[1] NA

get("200080_s_at", hgu133aSYMBOL)

[1] NA



--
Ulisse: "Considerate la vostra semenza:
fatti non foste a viver come bruti,
ma per seguir virtute e canoscenza".
(Dante, Divina Commedia, Canto XXVI)
--
G-C
T---A Luigi Marchionni, M.D., Ph.D.
C----G The Sidney Kimmel Comprehensive Cancer Center
G-------C Johns Hopkins University - School of Medicine
A------T 1550 Orleans St., CRB2, Rm 554
C----G Baltimore, MD, 21231, USA
G--C Tel: (001) 410-502-8179
C-G Fax: (001) 410-502-5742
T---A e-mail: marchion at jhmi.edu
G-----C URL: http://astor.som.jhmi.edu/~marchion/
A-------T