[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
>>
>>
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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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--
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
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