[BioC] Help with base file in AnnBuilder

Wed Nov 14 01:52:31 CET 2007

 Hi Marc,
This doesn't seem to be the problem as its an object so doesn't need the
quotes in the ABPkgBuilder command.  Adding quotes and calling it in the
command itself doesn't fix the problem either..

-----Original Message-----
From: Marc Carlson [mailto:mcarlson at fhcrc.org] 
Sent: Wednesday, 14 November 2007 12:46 p.m.
To: Johnstone, Alice
Cc: James W. MacDonald; bioconductor at stat.math.ethz.ch
Subject: Re: [BioC] Help with base file in AnnBuilder

Johnstone, Alice wrote:
> 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
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>   
Hi Alice,

>From reading your two posts I think that all you are missing might just
be the quotes around the filename that you are trying to pass in?

    Marc