[BioC] Help with base file in AnnBuilder

James MacDonald jmacdon at med.umich.edu
Wed Nov 14 02:58:44 CET 2007


Hi Alice,

If you can type something like

ABPkgBuilder(baseName=myBase, ...)

then what is being picked up by R is an object in the global workspace 
with that name rather than a text file. For it to find a text file you 
will have to pass a character string (hence the quotation marks).

Best,

Jim



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
>>
>>
>> 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.
>> _______________________________________________
>> Bioconductor mailing list
>> Bioconductor at stat.math.ethz.ch
>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>> Search the archives: 
>> http://news.gmane.org/gmane.science.biology.informatics.conductor
> 
> --
> 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
> 
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor

-- 
James W. MacDonald, MS
Biostatistician
UMCCC cDNA and Affymetrix Core
University of Michigan
1500 E Medical Center Drive
7410 CCGC
Ann Arbor MI 48109
734-647-5623



More information about the Bioconductor mailing list