[Bioc-devel] Different behavior of get() between 2.9.0 and later versions`
Thanks. I'll try to see whether if I build my mgug4122a.db package this happens. maybe the problem is in org.Mm.eg.db luigi
On Nov 4, 2009, at 12:54 AM, Seth Falcon wrote:
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
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