[BioC] Help with base file in AnnBuilder

[Johnstone, Alice]

My data file was in a tab-separated file, how do you read it without it
reading as a data.frame or matrix? 

-----Original Message-----
From: James W. MacDonald [mailto:jmacdon at med.umich.edu] 
Sent: Wednesday, 14 November 2007 11:30 a.m.
To: Johnstone, Alice
Cc: bioconductor at stat.math.ethz.ch
Subject: Re: [BioC] Help with base file in AnnBuilder

Hi Alice,

Johnstone, Alice wrote:
> 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")?

The base file is supposed to be a tab-separated _text file_ that
contains the (in this case) Affy IDs in the first column, and the Entrez
Gene IDs in the second. It appears here that you are using either a
matrix or a data.frame.

Does it work if you first do something like

write.table(myBase, "myBase", sep="\t", col.names=FALSE,
row.names=FALSE)

and then try again using

ABPkgBuilder(baseName="myBase", <otherargshere>)?

Best,

Jim


> 
>> 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"),f
> ro
> 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
> 
> 
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--
James W. MacDonald, M.S.
Biostatistician
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109
734-647-5623