[BioC] Affy TilingArray makePDpackage
Benilton Carvalho
bcarvalh at jhsph.edu
Sat Jun 9 20:21:40 CEST 2007
http://www.bioconductor.org/packages/2.1/bioc/html/affyio.html
On Jun 9, 2007, at 2:00 PM, joseph wrote:
> Hi Ben
> Is there a way for me to get affyio 1.5.4 now or I have to wait to
> the next BioC release?
> Thanks
> Joseph
>
> ----- Original Message ----
> From: Ben Bolstad <bmb at bmbolstad.com>
> To: joseph <jdsandjd at yahoo.com>
> Cc: James W. MacDonald <jmacdon at med.umich.edu>; Bioconductor
> <Bioconductor at stat.math.ethz.ch>
> Sent: Tuesday, June 5, 2007 9:39:37 PM
> Subject: Re: [BioC] Affy TilingArray makePDpackage
>
> I guess this is what I get for not reading the mailing list that
> closely
> these days (even when my name is mentioned).
>
> I think I have fixed this issue in affyio 1.5.4, let me know if it is
> still not working when ever the windows version gets built.
>
> Best,
>
> Ben
>
>
>
>
>
> On Tue, 2007-06-05 at 16:14 -0700, joseph wrote:
>> Has anybody figure out the solution to the following error:
>>> makePDpackage
>>> ("Mm_PromPR_v01_NCBIv35.bpmap",file1="Mm_PromPR_v02.cif",manufacture
>>> r="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)
>> i686-redhat-linux-gnu
>> locale:
>> LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_U
>> S.UTF-8;LC_MONETARY=en_US.UTF-8;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_U
>> S.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UT
>> F-8;LC_IDENTIFICATION=C
>> attached base packages:
>> [1] "splines" "tools" "stats" "graphics" "grDevices"
>> "utils"
>> [7] "datasets" "methods" "base"
>> other attached packages:
>> makePlatformDesign oligo BufferedMatrixMethods
>> "1.0.0" "1.0.2-3" "1.0.0"
>> BufferedMatrix RSQLite DBI
>> "1.0.0" "0.5-4" "0.2-3"
>> Biobase affyio
>> "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 <Bioconductor at stat.math.ethz.ch>; Ben Bolstad
>> <bmb at bmbolstad.com>
>> Sent: Wednesday, May 2, 2007 10:34:25 AM
>> Subject: Re: [BioC] Affy TilingArray makePDpackage
>> 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",manufactur
>>>> er="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",manufactur
>>>> er="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]]
>>
>>>
>>
>>>
>>
>>>
>>
>>>> _______________________________________________
>>
>>>
>>
>>>
>>
>>>> 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
>>
>>>
>>
>>>
>>
>>>
>>
>>>
>>
>>>
>>
>>>
>>
>>
>>
>>
>>
>
>
>
>
>
>
>
>
>
> ______________________________________________________________________
> ______________
>
>
> [[alternative HTML version deleted]]
>
> _______________________________________________
> 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
More information about the Bioconductor
mailing list