[BioC] annotation package for chicken affyprobes

[Lina Hultin-Rosenberg]

Hi Jim and Nianhua!

Thank you so much for your answers, perfect timing that the new AnnBuilder
version will support chicken!!

Yes Jim, my goal is to output a list of the top probesets along with
annotations as well as to be able to add gene names to volcano plots etc.
And later on also perhaps use the functional annotations, like GO, for some
analyses. I have quite a lot of annotation data in the annotation file
provided by affymetrix - mappings to different identifiers, functional
annotations etc. I might have everything I need there but I don't know how
to "connect" that to my affybatch or exprSet object or output from limma to
handle it easily. 


Thanks again!

Best,
Lina

-----Ursprungligt meddelande-----
Från: bioconductor-bounces at stat.math.ethz.ch
[mailto:bioconductor-bounces at stat.math.ethz.ch] För Nianhua Li
Skickat: den 17 augusti 2006 03:15
Till: bioconductor at stat.math.ethz.ch
Ämne: Re: [BioC] annotation package for chicken affyprobes

Hi, Lina,

We are lucky in case of chicken. I just updated AnnBuilder (v1.11.7) to
support Gallus gallus (taxon id 9031). You can get it from svn right
away or wait 2 days to download it from bioc website. Or if you want to
try it now, here is the changes:

================================================================
--- IPI.R       (new)
+++ IPI.R       (old)
@@ -21,8 +21,7 @@
     speciesNorganismTable <- rbind(
                                    c("human", "Homo sapiens"),
                                    c("mouse", "Mus musculus"),
-                                   c("rat", "Rattus norvegicus"),
-                                  c("chick", "Gallus gallus")
+                                   c("rat", "Rattus norvegicus")
                                    )
     colnames(speciesNorganismTable) <- c("species", "organism")
     return(speciesNorganismTable)
=================================================================
The above change happens in function "speciesNorganism". This allows you
get annotation for PFAM and PROSITE.

=================================================================
--- getSrcUrl.R (new)
+++ getSrcUrl.R (old)
@@ -65,7 +65,6 @@
                   "DANIO RERIO" = "Danio_Rerio",
                   "CAENORHABDITIS ELEGANS" = "Caenorhabditis_elegans",
                   "DROSOPHILA MELANOGASTER" = "Drosophila_melanogaster",
-                 "GALLUS GALLUS" = "Gallus_gallus",
                   NA)
     if(is.na(key)) {
         warning(paste("Organism", organism, "is not supported by
GoldenPath (GP)."))
@@ -170,7 +169,6 @@
       Sma = "Schistosoma mansoni", Ssa = "Salmo salar",
       Ssc = "Sus scrofa", Str = "Xenopus tropicalis",
       Xl = "Xenopus laevis", At = "Arabidopsis thaliana",
-      Gga = "Gallus gallus",
       Gma = "Glycine max", Han = "Helianthus annus",
       Hv = "Hordeum vulgare",  Lsa = " Lactuca sativa",
       Les = "Lycopersicon esculentum", Lco = "Lotus corniculatus",
==================================================================
The first change is in function "getUCSCUrl", for chromosome location.
The second is in function "UGSciNames" for UniGene.

I test it with this script:
===============================
library(AnnBuilder)
mypkg <- function(pkgPath, version) {
    ABPkgBuilder(baseName="mybase.txt",
                 baseMapType="ll",
                 pkgName="mypkg",
                 pkgPath=pkgPath,
                 organism="Gallus gallus",
                 version=version,
                 author=list(
                   authors="Nianhua Li",
                   maintainer="Nianhua Li<email at email.org>"
                   )
                 )
}
mypkg(getwd(), "1.0.0")
===============================

mybase.txt is
1       395929
2       395844
3       396017
4       415357
5       424377

QC data is:
Number of probes: 5
Probe number missmatch: None
Probe missmatch: None
Mappings found for probe based rda files:
         mypkgACCNUM found 0 of 5
         mypkgCHRLOC found 4 of 5
         mypkgCHR found 5 of 5
         mypkgENZYME found 4 of 5
         mypkgGENENAME found 0 of 5
         mypkgGO found 5 of 5
         mypkgLOCUSID found 5 of 5
         mypkgMAP found 0 of 5
         mypkgPATH found 5 of 5
         mypkgPMID found 3 of 5
         mypkgREFSEQ found 5 of 5
         mypkgSUMFUNC found 0 of 5
         mypkgSYMBOL found 5 of 5
         mypkgUNIGENE found 5 of 5
Mappings found for non-probe based rda files:
         mypkgENZYME2PROBE found 5
         mypkgGO2ALLPROBES found 107
         mypkgGO2PROBE found 19
         mypkgORGANISM found 1
         mypkgPATH2PROBE found 18
         mypkgPFAM found 5
         mypkgPMID2PROBE found 4
         mypkgPROSITE found 3

Let me know if you have any questions or concerns. Cheers!

nianhua

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