[BioC] Custom CDF for alternative splicing with xps

[Binbin [guest]]

Hello there, using xps and affymetrix official PGF files, I have built a scheme for hs exon_st1.0_v2 analysis at the transript level. Now we want to study isoforms by looking at the data at the exon level. One issue we want to avoid is the multiple-mapping of same probes and a reasonable up-to-date annotation. Brainarray's custom CDF (v16 Ensembl exon) seems a good choice. My question is - can import.expr.scheme() in xps build a root using these custom CDF files? Have gone through the xps reference/manual but still not sure.
Many thanks for suggestions.


 -- output of sessionInfo(): 

R version 2.15.0 (2012-03-30)
Platform: x86_64-unknown-linux-gnu (64-bit)

locale:
 [1] LC_CTYPE=en_US.utf8       LC_NUMERIC=C             
 [3] LC_TIME=en_US.utf8        LC_COLLATE=en_US.utf8    
 [5] LC_MONETARY=en_US.utf8    LC_MESSAGES=en_US.utf8   
 [7] LC_PAPER=C                LC_NAME=C                
 [9] LC_ADDRESS=C              LC_TELEPHONE=C           
[11] LC_MEASUREMENT=en_US.utf8 LC_IDENTIFICATION=C      

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] xps_1.18.0

loaded via a namespace (and not attached):
[1] tools_2.15.0


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