[BioC] Affy TilingArray makePDpackage

[James W. MacDonald]

Please don't take things off-list. We view the list archives as a useful 
source of information. I have re-sent to the list, but I don't know how 
to make Thunderbird respect the threading so this will appear as a new 
thread which is sub-optimal.

joseph wrote:
> Hi Jim
> Both files are in the working directory.  
> I just tried the same thing on my Windows machine. 

I get the same result. The error occurs at the line

bpmap <- .Call("ReadBPMAPFileIntoRList", bpmapFile, PACKAGE = "affyio")

so it appears there is a Windows-specific problem with the C code. This 
code was written by Ben Bolstad, so I am ccing him as well.

Best,

Jim
> 
> 
>>dir()
> 
> [1] "Mm_PromPR_v01_NCBIv35.bpmap" "Mm_PromPR_v02.cif"          
> 
>>makePDpackage("Mm_PromPR_v01_NCBIv35.bpmap",file1="Mm_PromPR_v02.cif",manufacturer="affymetrix", type="tiling")
> 
> affymetrix tiling 
> The package will be called pd.mm.prompr.v01.ncbiv35 
> Error in makeBPMAPenv(designFile, file1, genomebuild = genomebuild) : 
>         SET_VECTOR_ELT() can only be applied to a 'list', not a 'NULL'
> 
>>sessionInfo()
> 
> R version 2.5.0 (2007-04-23) 
> 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] "splines"   "tools"     "stats"     "graphics"  "grDevices" "utils"     "datasets"  "methods"   "base"     
> other attached packages:
>    makePlatformDesign                 oligo BufferedMatrixMethods        BufferedMatrix               RSQLite 
>               "1.0.0"               "1.0.2"               "1.0.0"               "1.0.0"               "0.5-3" 
>                   DBI               Biobase                affyio 
>               "0.2-2"              "1.14.0"               "1.4.0" 
> 
> 
> 
> 
> ----- Original Message ----
> From: James W. MacDonald <jmacdon at med.umich.edu>
> To: joseph <jdsandjd at yahoo.com>
> Cc: bioconductor at stat.math.ethz.ch
> Sent: Wednesday, May 2, 2007 8:52:56 AM
> Subject: Re: [BioC] Affy TilingArray makePDpackage
> 
> Hi Joseph,
> 
> 
> 
> joseph wrote:
> 
> 
>>Hi
> 
> 
> 
>>I upgraded to R 2.5.0 and Bioc 2.0.  When I tried to build a data package
> 
> 
>>for the mouse promoter tiling array, I got the following error message:
> 
> 
> 
>> makePDpackage("Mm_PromPR_v01_NCBIv35.bpmap",file1="Mm_PromPR_v02.cif",manufacturer="affymetrix", type="tiling")
> 
> 
>>affymetrix tiling 
> 
> 
>>The package will be called pd.mm.prompr.v01.ncbiv35 
> 
> 
>>Error in makeBPMAPenv(designFile, file1, genomebuild = genomebuild) : 
> 
> 
>>        SET_VECTOR_ELT() can only be applied to a 'list', not a 'NULL'
> 
> 
> 
> 
> That's odd. I just successfully did the same thing:
> 
> 
> 
>  > makePDpackage(dir()[14], dir()[15], manufacturer = "affymetrix", type 
> 
> = "tiling", extra=extra)
> 
> affymetrix tiling
> 
> The package will be called pd.mm.prompr.v01
> 
> Array identified as having 2166 rows and 2166 columns.
> 
> Creating package in /home/jmacdon/Desktop/pd.mm.prompr.v01
> 
> [1] "pd.mm.prompr.v01"
> 
>  > sessionInfo()
> 
> R version 2.5.0 (2007-04-23)
> 
> x86_64-unknown-linux-gnu
> 
> 
> 
> locale:
> 
> LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=en_US.UTF-8;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C
> 
> 
> 
> attached base packages:
> 
> [1] "splines"   "tools"     "stats"     "graphics"  "grDevices" "datasets"
> 
> [7] "utils"     "methods"   "base"
> 
> 
> 
> other attached packages:
> 
>     makePlatformDesign                 oligo BufferedMatrixMethods
> 
>                "1.0.0"               "1.0.2"               "1.0.0"
> 
>         BufferedMatrix               RSQLite                   DBI
> 
>                "1.0.0"               "0.5-3"               "0.2-2"
> 
>                Biobase                affyio
> 
>               "1.14.0"               "1.4.0"
> 
> 
> 
> Are both of the BPMAP and CIF files in your working directory?
> 
> 
> 
> Best,
> 
> 
> 
> Jim
> 
> 
> 
> 
> 
> 
> 
>>>sessionInfo()
> 
> 
>>R version 2.5.0 (2007-04-23) 
> 
> 
>>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] "splines"   "tools"     "stats"     "graphics"  "grDevices" "utils"     "datasets"  "methods"   "base"     
> 
> 
>>other attached packages:
> 
> 
>>   makePlatformDesign                 oligo BufferedMatrixMethods        BufferedMatrix               RSQLite 
> 
> 
>>              "1.0.0"               "1.0.2"              
> 
> 
>> "1.0.0"               "1.0.0"               "0.5-3" 
> 
> 
>>                  DBI               Biobase                affyio 
> 
> 
>>              "0.2-2"              "1.14.0"               "1.4.0" 
> 
> 
> 
>>Any help or suggestions will be appreciated.
> 
> 
>> Joseph
> 
> 
> 
> 
> 
>>__________________________________________________
> 
> 
> 
> 
> 
>>    [[alternative HTML version deleted]]
> 
> 
> 
>>_______________________________________________
> 
> 
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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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