[BioC] crlmm warning

[Morten Mattingsdal]

Hello again,
Ill just answer that myself, since I posted a bit too prematurely.
Seems like I need to use the makePlatformDesign package, with the code:

 > library(makePlatformDesign)
 > 
makePDpackage("Mapping50K_Xba240.CDF","Mapping50K_Xba240_probe_fasta","Mapping50K_Xba240_annot.csv",type="SNP")

R CMD INSTALL pdmapping50kxba240

I find it ... non-trivial.. to locate the fasta file for Nsp and Sty 
arrays, but I think Ill harass Affyemtrix Inc for that.

I am aware that the oligo package is in development, but It would be 
nice to have some vignettes to read

regards
morten




Morten Mattingsdal wrote:
> Hello everyone,
>
> Ive managed to get the oligo package and the crlmm function up and 
> running. Ive also installed the meta-data libraries from this URL 
> http://www.biostat.jhsph.edu/~bcarvalh/oligoAddOns.tar.gz
> provided by Benliton
>
> but when I run the commands:
>
>  >files <- list.celfiles()
>  >snpFSet <- read.celfiles(files)
>  >
>  >Welcome to the pd.Mapping250K_Nsp prototype pdInfo package
>  >WARNING: DO NOT USE THIS PACKAGE FOR ANY ANALYSIS.
>  >THIS PACKAGE IS FOR INTERFACE PROTOTYPE USE ONLY!
>  >THE DATA HAS NOT BEEN VALIDATED AND LIKELY HAS ERRORS.
>  >Have fun!
>
> Im am happy that this information is warning me, but to my point:
> - When will the "safe" mapping libraries come?
> - Can I build this by myself ?
>
> I want to compare brlmm from Affymetrix and crlmm from BioC genotype 
> calls for my data
>
> regards
> morten
>
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