[BioC] makePDpackage problem

Kasper Daniel Hansen khansen at stat.Berkeley.EDU
Wed Jun 20 23:43:00 CEST 2007

Hi Ingrid

The PDpackages are chip design packages for use with the oligo  
package. So far - as far as I know - the developers of that package  
has focussed on expression arrays and snp arrays, not tiling arrays.  
I could be wrong however. With the package you should be able to do  
stuff like quantile normalization and RMA like background correction  
because both of these approaches do not require a probe set (which  
the tiling arrays do not have).

Unless there are (new) functions in the oligo package dealing with  
the kind of analysis you are usually interested in when using tiling  
arrays (peak finding or segmentation), I believe you will have very  
to no use of the PDpackage you are in the process of creating, as  
both quantile normalization and rma like background correction is  
implemented in the affy package for a matrix. So the answer to your  
question is perhaps "you cannot use your PDpackage for much" (Note:  
this is written from my current knowledge of oligo, which is  
certainly not up to date). I am sure Benilton can fill us in on the  

Most of the infrastructure for snp and expression arrays from Affy  
centers around keeping track of probesets, something that does not  
make sense for tiling arrays.

If you are interested in doing a standard segmentation of your data,  
I would advise you to start with looking at the tilingArray package  
(and the companion data package davidTiling). The package contains a  
lot of useful code, but it is certainly not very user-friendly, so  
you might want to start looking at the two papers documenting the  
analysis implemented in the package to see if that is what you are  
interested in. The package does not use any of the PDpackage stuff,  
instead it reads everything into a standard ExpressionSet.

There might be other packages dealing with tiling array type data,  
but I don't know about them. Having said so, some of the segmentation  
algorithms from aCGH data (and associated packages) might also be  


On Jun 20, 2007, at 7:15 AM, Ingrid H. G. Østensen wrote:

> Hi
> I have looked in the archives and found out that I can use  
> makePDpackage to make platform design packages for my GeneChip S.  
> Pombe Tiling 1.0FR Array, but I have gotten some problems and  
> questions.
> My question is: What can I do with my data after I have made this  
> package?
> My problem: When I try to run the command I get the following error.
>> makePDpackage("Sp20b_M_v04.bpmap", file1 = "Sp20b_M_v04.cif",  
>> manufacturer = "affymetrix",type="tiling")
> affymetrix tiling
> The package will be called pd.sp20b.m.v04
> Error in makeBPMAPenv(designFile, file1, genomebuild = genomebuild) :
>         SET_VECTOR_ELT() can only be applied to a 'list', not a 'NULL'
> My session info is as follows:
>> sessionInfo()
> R version 2.5.0 (2007-04-23)
> i386-pc-mingw32
> locale:
> LC_COLLATE=Norwegian (Bokmål)_Norway.1252;LC_CTYPE=Norwegian  
> (Bokmål)_Norway.1252;LC_MONETARY=Norwegian (Bokmål)_Norway. 
> 1252;LC_NUMERIC=C;LC_TIME=Norwegian (Bokmål)_Norway.1252
> attached base packages:
>  [1] "grid"      "splines"   "tools"     "stats"     "graphics"   
> "grDevices" "utils"     "datasets"  "methods"   "base"
> other attached packages:
>    makePlatformDesign                 oligo  
> BufferedMatrixMethods        BufferedMatrix               RSQLite
>               "1.0.0"             "1.0.2-3"                
> "1.0.0"               "1.0.0"               "0.5-4"
>                   DBI           tilingArray                 
> pixmap                   vsn                 limma
>               "0.2-3"              "1.14.0"                
> "0.4-7"               "2.2.0"              "2.10.0"
>           strucchange              sandwich                    
> zoo          affyQCReport           geneplotter
>               "1.3-2"               "2.0-2"                
> "1.3-1"              "1.14.0"              "1.14.0"
>               lattice              annotate           
> RColorBrewer               affyPLM                 gcrma
>              "0.15-8"              "1.14.1"                
> "0.2-3"              "1.12.0"               "2.8.0"
>           matchprobes              affydata                 
> xtable            simpleaffy            genefilter
>               "1.8.1"              "1.11.2"                
> "1.4-6"             "2.10.11"              "1.14.1"
>              survival                  affy                 
> affyio               Biobase
>                "2.31"              "1.14.0"                
> "1.4.0"              "1.14.0"
> 	[[alternative HTML version deleted]]
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