Entering edit mode
Hello all,
I tried to build annotation with AnnBuilder package.
The base file I used has probe names and mapped Entrez
Gene IDs (human genes). Things worked fine, except
some failed connection to KEGG database. And I got the
final annotation package, and it works, that is really
cool. However, I didn't see the gene information data,
like "GENENAME", "SYMBOL" etc, though. And this
information is important for a complete annotation of
my customized microarray platform.
I looked at annotation packages for affy chips, all
have gene information data. However, the whole human
genome annotation package, humanLLMappings, doesn't
have it. And since these are also built with
AnnBuilder, I think something stop working properly in
my case and in humanLLMappings' case.
I studied the source codes from AnnBuilder package,
and narrowed the problem down to the corresponding
part in getAnnData function, which is called in
ABPkgBuilder function. Here is that code chunk I
extraced:
parser(srcObjs[["eg"]]) <-
getBaseParsers("eginfo")
geneinfo <- try(parseData(srcObjs[["eg"]],
srcObjs[["eg"]]@info,
ncol = 5, mergeKey = FALSE))
colnames(geneinfo) <- c("PROBE", "SYMBOL",
"GENENAME", "CHR",
"MAP")
options(show.error.messages = TRUE)
if (inherits(annotation, "try-error")) {
stop(paste("Parsing Entrez Gene gene_info.gz
failed because of:\n\n",
annotation))
}
if (nrow(geneinfo) > 0)
annotation <- merge(annotation, geneinfo, by =
"PROBE",
all.x = TRUE)
I am not sure what problem happens here, but there is
no error message shown, and which means I did get
something assigned to geneinfo, but geneinfo is not
merge into annotation, very likely it has 0 rows.
I am not sure I am correct here, but please let me
know if you have any idea, and you know how to solve
this problem. Thank you so much in advance.
Here is the code I use to build my annotation
??
ABPkgBuilder(baseName = myBase, baseMapType =
myBaseType,
pkgName = "hs95av2Entrezg7", pkgPath = myDir,
organism = "Homo sapiens", version = "1.1.0", author =
list(authors = "Weijun",
maintainer = "Weijun <luo_weijun at="" yahoo.com="">"), fromWeb
=T)
print(date())
And my sessionInfo
Version 2.3.1 (2006-06-01)
powerpc-apple-darwin8.6.0
attached base packages:
[1] "tools" "methods" "stats" "graphics"
"grDevices" "utils"
[7] "datasets" "base"
other attached packages:
AnnBuilder RSQLite DBI annotate XML
Biobase
"1.10.0" "0.4-1" "0.1-10" "1.10.0" "0.99-7"
"1.10.0"
Weijun
