[BioC] package pair "hugene10stv1cdf"/"hugene10stprobeset.db"

[Laurent Gautier]

Dear List,

I am noting potential issues in the package pair  
"hugene10stv1cdf"/"hugene10stprobeset.db", as the respective sets of 
probe set IDs are not overlapping:

 > library(hugene10stv1cdf)
 > library(hugene10stprobeset.db)
 > summary(ls(hugene10stv1cdf) %in% Lkeys(hugene10stprobesetSYMBOL))
    Mode   FALSE    TRUE    NA's
logical   28026    4295       0
 > summary(Lkeys(hugene10stprobesetSYMBOL) %in% ls(hugene10stv1cdf))
    Mode   FALSE    TRUE    NA's
logical  252727    4295       0

Reading closely, one can observe that "hugene10stprobeset.db" refers to 
a "revision 5" while the "v1" in "hugene10stv1cdf" suggests a revision 
1. It is unclear to me whether this is linked to the problem, but if so 
then there is no hugene10stv5cdf, neither annotation for v1.

The obligatory sessionInfo() is:

 > sessionInfo()
R version 2.11.0 Patched (2010-04-24 r51813)
i686-pc-linux-gnu

locale:
  [1] LC_CTYPE=en_GB.utf8       LC_NUMERIC=C
  [3] LC_TIME=en_GB.utf8        LC_COLLATE=en_GB.utf8
  [5] LC_MONETARY=C             LC_MESSAGES=en_GB.utf8
  [7] LC_PAPER=en_GB.utf8       LC_NAME=C
  [9] LC_ADDRESS=C              LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_GB.utf8 LC_IDENTIFICATION=C

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
  [1] oligo_1.12.0                AffyCompatible_1.8.0
  [3] RCurl_1.4-1                 bitops_1.0-4.1
  [5] XML_2.8-1                   oligoClasses_1.10.0
  [7] limma_3.4.0                 hugene10stv1cdf_2.6.0
  [9] hugene10stprobeset.db_5.0.1 org.Hs.eg.db_2.4.1
[11] RSQLite_0.8-4               DBI_0.2-5
[13] AnnotationDbi_1.10.0        affxparser_1.20.0
[15] affy_1.26.0                 Biobase_2.8.0

loaded via a namespace (and not attached):
[1] affyio_1.16.0         Biostrings_2.16.0     IRanges_1.6.0
[4] preprocessCore_1.10.0 splines_2.11.0        tcltk_2.11.0
[7] tools_2.11.0
 >

Best,


Laurent