[BioC] Tiling arrays and their probes

[Steve Lianoglou]

Hi folks,

I just wanted to thank you for replying to my original message. I had  
my gmail filters set up incorrectly to tag bioconductor mails and your  
responses never popped up on my radar in my email client (that I'm  
using to read gmail), so all this time I thought my questions were  
going unanswered. I didn't want to give the impression that my silence  
== ungratefulness.

So .. thanks again. I'll look into the hints that were given and  
follow up with any more questions that I can't figure out.

> the CDF structure (i.e. file or package) is only useful if you want  
> to analyse cDNA or RNA hybridisation tiling array data for overall  
> mRNA abundances using the existing genome annotation. Most people  
> use tiling arrays for additional tasks, e.g. transcript discovery  
> and "fine-mapping", or ChIP-chip (you didn't say what your use case  
> is).

Btw, I think what I'm doing probably falls into fine-mapping, for  
now... although this is a new term to me, it sounds more like what I'm  
after than transcript discovery for the moment.

> If you want to use the mapping provided by Affymetrix, then I think  
> the "affxparser" package is a good start point, but for converting  
> its output to a "probeAnno" object afaIk you're on your own (perhaps  
> some good soul wants to contribute a function for that?)

Once I get passed that "fat-fingers" feeling I get as an R neophyte,  
I'd be happy to contribute something like this back since its  
something I think I might need for a first pass analysis, anyway.

Thanks,
-steve