[BioC] Help with base file in AnnBuilder

[Johnstone, Alice]

Hi 
I have been trying to create a annotation package but have become stuck
with my base file.  I am not sure what format it needs to be in.  Also
could someone clarify what a "map" is? Ie what the help files ask for to
be in the second column of the base file, is this just the accession
numbers, genebank ids etc? (from the helpfile "the second one being the
maps to GenBank accession numbers")?

> ABPkgBuilder(baseName=myBase,srcUrls=mySrcUrls,baseMapType="ll",
+ pkgName="rats",pkgPath=myDir,organism="Rattus
norvegicus",version="1.1.0",
+
author=list(authors="Alice",maintainer="alice.johnstone at esr.cri.nz"),fro
mWeb=TRUE)
Error in getBaseFile(baseName) : 
  Base file c("1397882_at", "1394539_at", "1397115_at", "1369569_at",
"1389862_at", "1383230_at", "1389175_at", "1372644_at", "1378579_at",
"1375210_at", "1398872_at", "1371842_at", "1392240_at", "1369133_a_at",
"1370123_a_at", "1395529_at", "1398185_at", "1384220_at", "1387589_at",
"1373634_at", "1376280_at", "1379569_at", "1396519_at", "1372832_at",
"1368260_at", "1372145_at", "1382644_at", "1388579_at", "1385210_at",
"1381842_at", "1374624_at", "1376349_a_at", "1373822_at", "1394220_at",
"1397589_at", "1369250_at",  may not be valid or have two columnsBase
file c("313049", "64572", "360937", "65140", "362955", "360664",
"305455", "686765", NA, NA, "161477", "679898", NA, "117101", "60465",
NA, "306424", "316221", "65025", NA, NA, NA, "24418", NA, "114592",
"294810", NA, "689414", "305987", "293024", "311952", "65194", "303740",
"316012", NA, "116642", "619440", "300446", "366792", "294799",
"688699", "298594", "24172", "303787", NA, "114561", "305895", "498331",
"361256", NA
> 
> traceback()
4: stop(paste("Base file", baseName, "may not be valid or have two
columns"))
3: getBaseFile(baseName)
2: getUniMappings(baseName, srcObjs[["eg"]], srcObjs[["ug"]], NULL, 
       baseMapType)
1: ABPkgBuilder(baseName = myBase, srcUrls = mySrcUrls, baseMapType =
"ll", 
       pkgName = "rats", pkgPath = myDir, organism = "Rattus
norvegicus", 
       version = "1.1.0", author = list(authors = "Alice", maintainer =
"alice.johnstone at esr.cri.nz"), 
       fromWeb = TRUE)
> str(myBase)
'data.frame':   53622 obs. of  2 variables:
 $ V1: chr  "1397882_at" "1394539_at" "1397115_at" "1369569_at" ...
 $ V2: chr  "313049" "64572" "360937" "65140" ...
> sessionInfo()
R version 2.7.0 Under development (unstable) (2007-11-10 r43420) 
i386-pc-mingw32 

locale:
LC_COLLATE=English_New Zealand.1252;LC_CTYPE=English_New
Zealand.1252;LC_MONETARY=English_New
Zealand.1252;LC_NUMERIC=C;LC_TIME=English_New Zealand.1252

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

other attached packages:
 [1] GO_2.0.1            lumiRatV1_1.3.1     rat2302_2.0.1
AnnBuilder_1.17.0   annotate_1.17.2    
 [6] xtable_1.5-2        AnnotationDbi_1.1.6 RSQLite_0.6-4
DBI_0.2-4           XML_1.9-0          
[11] Biobase_1.17.4     
> 



Alice Johnstone

PhD Student
Institute of Environmental Science and Research Ltd
Kenepuru Science Centre
34 Kenepuru Drive
PO Box 50-348
Porirua
New Zealand

Tel:  + 64 4 914-0717
Fax: + 64 4 914-0770


P Think before you print
This e-mail transmission and any attachments that accompany it may contain information that is privileged, confidential or otherwise exempt from disclosure under applicable law and is intended solely for the use of the individual(s) to whom it was intended to be addressed.
If you have received this e-mail by mistake, or you are not the intended recipient, any disclosure, dissemination, distribution, copying or other use or retention of this communication or its substance is prohibited. If you have received this communication in error, please immediately reply to the author via e-mail that you received this message by mistake and also permanently delete the original and all copies of this e-mail and any attachments from your computer. Thank you.