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

Seth Falcon seth at userprimary.net
Wed Nov 4 06:54:18 CET 2009


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
>
> _______________________________________________
> Bioc-devel at stat.math.ethz.ch mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel



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