[BioC] Selecting probe pairs for analysis

[Hee Siew Wan]

Hi All,
 
I'm interested in calculating the expression measure using only 8 pairs of probes from each probe set of Arabidopsis genechip (i.e instead of using the whole 11 pairs of a probe set). After searching through the archive, I found that I can create a new cdf environment that excludes the pairs that I'm not interested in. However, when I tried using makecdfenv to create the new CDF package, I get a Segmentation fault. I'm using R Version 1.9.0 (2004-04-12) on UNIX platform.
 
I understand that the error occurs due to the file that I have. I have a ATH1-121501.CDF of type Channel Definition File (which I didn't have problem reading) and I modified this file by deleting 1 pair of probes from 266455_at. I saved it as another .CDF. I opened the file using EditPadLite Version 5.3.0 and did the modification from there as well. I'm not very sure where did I make mistake(s). I'd appreciate any comment on this.
 
Is there another way of reading certain probe pairs instead of deleting them in the CDF? I'd appreciate any help. Thanks.
 
Cheers
siew wan