[BioC] Affy TilingArray makePDpackage

[James W. MacDonald]

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
> 
> 
> 
> __________________________________________________
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-- 
James W. MacDonald
Affymetrix and cDNA Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
734-647-5623


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