[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
>>>>     
>>>>       
>>> 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 
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>>>     
>> computer. Thank you.
>>   
>>>   
>>>     
>>>> _______________________________________________
>>>> Bioconductor mailing list
>>>> Bioconductor at stat.math.ethz.ch
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>>>> 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
>>>
>>>   
>>>     
>> 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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