[BioC] custom PM only chips and CDF files

[Kasper Daniel Hansen]

On Dec 5, 2005, at 11:24 AM, Stephen Henderson wrote:

>
> Hello
> I am interested to hear if anyone has had experience of using  
> custom PM only chips (Affymetrix-for expression) together with  
> Bioconductor?
>
> In particular I'd like to know if there are any special  
> arrangements needed for the CDF file (formatting changes etc) or if  
> this works seemlessly with the affy Packages for instance?
>
> I don't foresee any problems but thought it would be prudent to ask  
> on this forum to avoid unpleasant surprises.

I have no practical experience, but there should really be no problem  
as long as you avoid routines which requires MM probes (like GCRMA  
and Mas5).

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.

I do not mind helping with this, if I can get a copy of the cdf  
file.  It would be nice to have this functionality out of the box in  
affxparser.

Kasper Daniel Hansen

> Stephen Henderson
>
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