[BioC] error in hugene10sttranscriptcluster
Javier Pérez Florido
jpflorido at gmail.com
Sat Apr 16 14:15:45 CEST 2011
Dear list,
I'm trying to get the ENTREZIDs of some Affy_IDs of GeneChip Human Gene
ST 1.0 Arrays through hugene10sttranscriptcluster package. Depending on
the R version, the results are different.
For example, in R 2.12.2:
> mget("8104901",hugene10sttranscriptclusterENTREZID)
$`8104901`
[1] "3575"
But
>mget("8019631",hugene10sttranscriptclusterENTREZID)
Error en .checkKeys(value, Lkeys(x), x at ifnotfound) :
value for "8019631" not found
The sessionInfo is:
sessionInfo()
R version 2.12.2 (2011-02-25)
Platform: x86_64-pc-mingw32/x64 (64-bit)
locale:
[1] LC_COLLATE=Spanish_Spain.1252 LC_CTYPE=Spanish_Spain.1252
[3] LC_MONETARY=Spanish_Spain.1252 LC_NUMERIC=C
[5] LC_TIME=Spanish_Spain.1252
attached base packages:
[1] grid tools tcltk stats graphics grDevices utils
[8] datasets methods base
other attached packages:
[1] annotate_1.28.1 oneChannelGUI_1.16.5
[3] girafe_1.2.0 genomeIntervals_1.6.0
[5] intervals_0.13.3 ShortRead_1.8.2
[7] lattice_0.19-17 Rsamtools_1.2.3
[9] Biostrings_2.18.4 GenomicRanges_1.2.3
[11] baySeq_1.4.0 edgeR_2.0.5
[13] IRanges_1.8.9 preprocessCore_1.12.0
[15] GOstats_2.16.0 graph_1.28.0
[17] Category_2.16.1 tkWidgets_1.28.0
[19] DynDoc_1.28.0 widgetTools_1.28.0
[21] affylmGUI_1.24.0 affyio_1.18.0
[23] affy_1.28.0 limma_3.6.9
[25] hugene10sttranscriptcluster.db_6.0.1 org.Hs.eg.db_2.4.6
[27] RSQLite_0.9-4 DBI_0.2-5
[29] AnnotationDbi_1.12.0 Biobase_2.10.0
loaded via a namespace (and not attached):
[1] BSgenome_1.18.3 genefilter_1.32.0 GO.db_2.4.5 GSEABase_1.12.2
[5] hwriter_1.3 RBGL_1.26.0 splines_2.12.2 survival_2.36-5
[9] XML_3.2-0.2 xtable_1.5-6
However, in R 2.10.0
mget("8104901",hugene10sttranscriptclusterENTREZID)
$`8104901`
[1] "3575" (the same as before in R 2.12.2)
> mget("8019631",hugene10sttranscriptclusterENTREZID)
$`8019631`
[1] "6066" (there is no error like in R 2.12.2)
The sessionInfo is:
R version 2.10.0 (2009-10-26)
i386-pc-mingw32
locale:
[1] LC_COLLATE=Spanish_Spain.1252 LC_CTYPE=Spanish_Spain.1252
[3] LC_MONETARY=Spanish_Spain.1252 LC_NUMERIC=C
[5] LC_TIME=Spanish_Spain.1252
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] limma_3.2.3
hugene10sttranscriptcluster.db_4.0.1
[3] org.Hs.eg.db_2.3.6 RSQLite_0.9-2
[5] DBI_0.2-5 AnnotationDbi_1.8.2
[7] Biobase_2.6.1
loaded via a namespace (and not attached):
[1] tools_2.10.0
Why this error for Affy_ID 8019631 when R2.12.2 is used?
Thanks,
Javier
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