Question: AnnBuilder problem
0
gravatar for Yihuan Xu
11.9 years ago by
Yihuan Xu130
Yihuan Xu130 wrote:
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
organism annotate annbuilder • 447 views
ADD COMMENTlink written 11.9 years ago by Yihuan Xu130
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