[BioC] Help on mapping10xba142

[Zhang, Jacob (Zhongfa)]

Dear All:

Thank you  all for your timely and valuable suggestions in trying to
help out in installing the mapping10kxbar142 to R.   Unfortunately, none
worked though.  The most promising method given by James attached below
worked well until the   last step that need to build an R-package.  When
in R I trye: 

>makePDpackage("Mapping10K_Xba142.cdf","Mapping10K_Xba142.csv", 
"Mapping10K_Xba142_probe_fasta", type = "SNP")

R gave:
>>>>>>>>>>
Assuming Affymetrix Chip
The package will be called pdmapping10kxba142 
SNP Array
Reading Mapping10K_Xba142.cdf 
Magic number is not 67. This is probably not a binary cdf file.
>>>>>>>>>>>

Any suggestions?

Thanks, 

Jacob Zhang
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
Original suggestions:
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
It is simple to do. First install R-2.2.0dev, run biocLite() to install 
necessary packages, then install.packages2("makePlatformDesign", 
getAllDeps = TRUE).

Next, get these two files

http://www.affymetrix.com/Auth/analysis/downloads/taf/Mapping10K_Xba142_
annot_csv.zip
http://www.affymetrix.com/Auth/analysis/downloads/data/Mapping10K_Xba142
_probe_fasta.zip

put these in the same directory (after unzipping) as your cdf file (this

should be your working directory).

Then type
makePDpackage("Mapping10K_Xba142.cdf","Mapping10K_Xba142.csv", 
"Mapping10K_Xba142_probe_fasta", type = "SNP")

This will make a package that you can install using R CMD INSTALL. If 
you are on Linux, you can install this directly. If you are on windows 
or MacOS you may need to get some tools. See the R-FAQ for these 
operating systems.

As Rafa noted in an earlier response to your email, you would then need 
the oligo package to analyze these data. Since we are still actively 
working on this package, things are not well documented so it will take 
some work on your part to do any analyses.

HTH,

Jim      
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