[BioC] Help with base file in AnnBuilder
James W. MacDonald
jmacdon at med.umich.edu
Wed Nov 14 18:16:46 CET 2007
Hi Alice,
Using your code, I get the following results:
> a <- 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")
> b <- 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)
These are different lengths, so
> write.table(cbind(a, b[1:36]), "myBase", quote=F, sep="\t",
col.names=F, row.names=F)
> mySrcUrls <- getSrcUrl("all", "Rattus norvegicus")
> ABPkgBuilder(baseName="myBase", srcUrls=mySrcUrls, baseMapType="ll",
pkgName="rats", organism="Rattus norvegicus", version="0.0.1",
pkgPath=getwd(), author=list(authors="me", maintainer="me
<me at mine.com>"), fromWeb=TRUE)
[snip]
Then I installed using R CMD INSTALL
> library(rats)
> rats()
Quality control information for rats
Date built: Created: Wed Nov 14 12:06:00 2007
Number of probes: 36
Probe number missmatch: None
Probe missmatch: None
Mappings found for probe based rda files:
ratsACCNUM found 0 of 36
ratsCHR found 26 of 36
ratsCHRLOC found 20 of 36
ratsENTREZID found 26 of 36
ratsENZYME found 0 of 36
ratsGENENAME found 26 of 36
ratsGO found 20 of 36
ratsMAP found 25 of 36
ratsPATH found 0 of 36
ratsPMID found 17 of 36
ratsREFSEQ found 26 of 36
ratsSUMFUNC found 0 of 36
ratsSYMBOL found 26 of 36
ratsUNIGENE found 23 of 36
Mappings found for non-probe based rda files:
ratsCHRLENGTHS found 21
ratsGO.1 found 0
ratsGO2ALLPROBES found 345
ratsGO2PROBE found 106
ratsORGANISM found 1
ratsPFAM found 18
ratsPMID2PROBE found 94
ratsPROSITE found 14
> sessionInfo()
R version 2.6.0 beta (2007-09-24 r42966)
i386-pc-mingw32
locale:
LC_COLLATE=English_United States.1252;LC_CTYPE=English_United
States.1252;LC_MONETARY=English_United
States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252
attached base packages:
[1] stats graphics grDevices datasets utils methods base
other attached packages:
[1] rats_0.0.1 rcompgen_0.1-15
loaded via a namespace (and not attached):
[1] Biobase_1.16.0 tools_2.6.0
Best,
Jim
Johnstone, Alice wrote:
> It is the code in the vignette that I have been following (ABPrimer) ..
> Although when I try this exactly using the example base file I still get
> the following error
>
>> ABPkgBuilder(baseName = "myBase", srcUrls = mySrcUrls, baseMapType =
> + myBaseType, pkgName = "hgu95av2",
> + pkgPath = myDir, organism = "Homo sapiens", version = "1.1.0",
> + author = list(authors = "myname", maintainer =
> + "myname at myemail.com"), fromWeb = TRUE)
> Error in getBaseFile(baseName) :
> Base file myBase may not be valid or have two columns
>
> -----Original Message-----
> From: Marc Carlson [mailto:mcarlson at fhcrc.org]
> Sent: Wednesday, 14 November 2007 2:37 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:
>> 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
>>>>
>>>>
>>>> P Think before you print
>>>> This e-mail transmission and any attachments that accompany it may
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>>>>
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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
>>>
>>> _______________________________________________
>>> Bioconductor mailing list
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>>> Search the archives:
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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
--
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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