[BioC] crlmm warning
mortenm at inbox.com
Wed Mar 7 13:10:59 CET 2007
Ill just answer that myself, since I posted a bit too prematurely.
Seems like I need to use the makePlatformDesign package, with the code:
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
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
> 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
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