[BioC] custom PM only chips and CDF files

[Kasper Daniel Hansen]

On Dec 6, 2005, at 7:40 AM, Ben Bolstad wrote:

>
>> You may have problems constructing the cdf environment using the
>> stuff in the makecdfenv package. As I recall, the code explicitely
>> tries to find the the two probes in a probepair. If you use that
>> package make sure that you check what you get. You should at least be
>> able to parse the file using the affxparser package and then you will
>> need to do some post-processing to actually construct the cdf env.
>>
>
> Actually the functions for making cdfenv packages and environments in
> makecdfenv should quite happily process a CDF file with PM only
> probesets. I have done it a number of times in the past, so you should
> not have any problems.

That is good to hear. As I wrote, I do not have practical experience  
with PM only chips.

I do have experience with a custom chip where the 13 base of the MM  
probe is not (necessarily) the complement of the corresponding PM  
base, but just one of the 3 possible other bases. In that case the  
makecdfenv functions parses the CDF file and seemingly returns a  
proper object. Closer inspection reveals it is wrong however. But  
that is a particular degenerate example.

Kasper