[BioC] Help with base file in AnnBuilder

Marc Carlson mcarlson at fhcrc.org
Wed Nov 14 02:37:26 CET 2007


Johnstone, Alice wrote:
>  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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>>>       
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>   
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>>   
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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
>>
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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

Yes well it's not supposed to be an R object.  It needs to be a
tab-delimited file instead. 

James had a good suggestion for you to write your object back out to a
file so that you could then feed that file to the function.


Have you seen that there is documentation for AnnBuilder located on this
page?

http://bioconductor.org/packages/2.1/bioc/html/AnnBuilder.html


hope this helps you,


    Marc



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