[BioC] missing probe_id in ath1121501.db

[suganya [guest]]

Already in reference to the post in biocondcutor mailing list (https://stat.ethz.ch/pipermail/bioconductor/2012-February/043741.html) , Iam facing the same issues:

universe<-mget(c("244901_at", "244902_at", "244903_at", "244904_at", "244905_at", 
+              "244906_at", "244907_at", "244908_at", "244909_at", "244910_s_at", 
+              "244911_at", "244912_at", "244913_at", "244914_at", "244915_s_at", 
+              "244916_at", "244917_at", "244918_at", "244919_at", "244920_s_at", 
+              "244921_s_at", "244922_s_at", "244923_s_at", "244924_at", "244925_at", 
+              "244926_s_at", "244927_at", "244928_s_at", "244929_at", "244930_at", 
+              "244931_at", "244932_at", "244933_at", "244934_at", "244935_at", 
+              "244936_at", "244937_at", "244938_at", "244939_at", "244940_at", 
+              "244941_at", "244942_at", "244943_at", "244944_s_at", "244945_at", 
+              "244946_at", "244947_at", "244948_at", "244949_at", "244950_at", 
+              "244951_s_at", "244952_at", "244953_s_at", "244954_s_at", "244955_at", 
+              "244956_s_at", "244957_at", "244958_at", "244959_s_at", "244960_at", 
+              "244961_at", "244962_at", "244963_at", "244964_at", "244965_at", 
+              "244966_at", "244967_at", "244968_at", "244969_at", "244970_at", 
+              "244971_at", "244972_at", "244973_at", "244974_at", "244975_at", 
+              "244976_at", "244977_at", "244978_at", "244979_at", "244980_at", 
+              "244981_at", "244982_at", "244983_at", "244984_at", "244985_at", 
+              "244986_at", "244987_s_at", "244988_s_at", "244989_s_at", "244990_s_at", 
+              "244991_s_at", "244992_s_at", "244993_s_at", "244994_at", "244995_at")

selected<-mget(c("244901_at", "244910_s_at", "245000_at", "245001_at", "245002_at", 
+              "245003_at", "245004_at", "245005_at", "245006_at", "245007_at", 
+              "245008_at", "245009_at", "244911_at", "245010_at", "245011_at")

params <- new("GOHyperGParams", geneIds = selected, universeGeneIds = universe, annotation="ath1121501", 
+               ontology = "MF", pvalueCutoff = 0.5, conditional = FALSE, testDirection = "over")
hgOver <- hyperGTest(params)

head(summary(hgOver), n = 1)
      GOMFID      Pvalue OddsRatio ExpCount Count Size    Term
1 GO:0005488 0.006822516   2.87234 20.08571    27   38 binding

The above works but when I intend to use it for the whole data as follows it fails:
universe <- unlist(mget(myd, ath1121501ACCNUM))

Error in .checkKeys(value, Lkeys(x), x at ifnotfound) : 
  value for "245651_s_at" not found

length(as.list(toggleProbes(ath1121501ACCNUM,"all")))

[1] 22809 # whereas there should be 22810 as in the chip.



 -- output of sessionInfo(): 

R version 2.15.2 (2012-10-26)
Platform: i686-redhat-linux-gnu (32-bit)

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C               LC_TIME=en_US.UTF-8
 [4] LC_COLLATE=en_US.UTF-8     LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
 [7] LC_PAPER=C                 LC_NAME=C                  LC_ADDRESS=C
[10] LC_TELEPHONE=C             LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

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

other attached packages:
 [1] annaffy_1.28.0       KEGG.db_2.7.1        GO.db_2.7.1          GOstats_2.22.0       graph_1.34.0
 [6] Category_2.22.0      ath1121501.db_2.7.1  org.At.tair.db_2.7.1 RSQLite_0.10.0       DBI_0.2-5
[11] AnnotationDbi_1.18.4 BiocInstaller_1.4.9  limma_3.12.3         affy_1.34.0          Biobase_2.16.0
[16] BiocGenerics_0.2.0

loaded via a namespace (and not attached):
 [1] affyio_1.22.0         annotate_1.34.1       genefilter_1.38.0     GSEABase_1.18.0
 [5] IRanges_1.14.4        preprocessCore_1.18.0 RBGL_1.32.1           splines_2.15.2
 [9] stats4_2.15.2         survival_2.36-14      tools_2.15.2          XML_3.9-4
[13] xtable_1.6-0          zlibbioc_1.2.0

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