[BioC] error in hugene10sttranscriptcluster

[James MacDonald]

Hi Javier,

The annotation of Affy chips tends to change over time, and this might
be an instance of that. If you check netaffx for this probeset, the
transcript it measures is described as 'multiple', and if you blat the
sequence they built the probeset against, it matches all over the place.
So it may be that in the past they claimed a direct match and now they
don't. 

You could investigate this further by looking at older versions of the
annotation files if you care to know more.

Best,

Jim



James W. MacDonald, M.S.
Biostatistician
Douglas Lab
5912 Buhl
1241 E. Catherine St.
Ann Arbor MI 48109-5618
734-615-7826
>>> Javier Pérez Florido 04/16/11 8:16 AM >>>
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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