[BioC] AnnBuilder problem

[Yihuan Xu]

Dear all,

I used AnnBuilder to annotate a customed array. One of gene is pla2g2a, its 
Access number is NM_011108, its ID number
in my array is 4842. however I could not get its symbol from the annotation 
package I made, neither in the KEGG pathway (mmu00590) it should belongs.

Following is my code:

myBase <- "C:\\annBuilder\\annotation"
myBaseType <-'gb'
mySrcUrls <- getSrcUrl("all", "Mus musculus")
myDir <- "C:\\annbuilder"
ABPkgBuilder(baseName = myBase, srcUrls = mySrcUrls, baseMapType =
myBaseType,  pkgName = "custommice",
pkgPath = myDir, organism = "Mus musculus", version = "1.2.0",
author = list(authors = "Yihuan Xu",
maintainer = "Yihuan XU <yihuan.xu at jefferson.edu>"), fromWeb = TRUE)

Here is my base file:

.......

4841 NM_011741
4842 NM_011108
4843 NM_008358
4844 NM_013538
4845 AF253409

.......

> xx <- as.list(custommiceSYMBOL)
> xx$'4842'
[1] NA
> aa <- as.list(custommiceACCNUM)
> aa$'4842'
[1] "NM_011108"
> bb <- as.list(custommicePATH2PROBE)
> bb$'00590'
 [1] "13561" "15263" "9739"  "5867"  "5868"  "13611" "13612" "20392" "12154"
[10] "7523"  "11395" "13076" "17435" "18165" "1460"  "15265" "6785"  "19134"
[19] "9204"  "12848" "20819" "19897" "5332"  "1032"  "17261" "21133" "18719"
[28] "19623" "806"   "13389" "1026"  "8774"  "8773"  "12645" "20857" "9740"
[37] "10428" "13682" "4411"  "18952" "13124" "539"   "22323" "2963"  "4902"
[46] "16517" "9046"  "4364"  "16505" "2066"  "3464"  "15080" "4410"  "19622"
[55] "9252"  "10708" "492"   "5297"  "17265" "1713"  "22039" "18172" "5104"
[64] "10421" "1232"  "11391" "7062"  "2679"


Do you have any idea what happened here?

Thank you very much.



Yihuan