[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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