[BioC] The metadata in an Affymetrix CDF

Steve Lianoglou mailinglist.honeypot at gmail.com
Tue May 27 19:44:35 CEST 2008

> 1) feature_ID is indeed pairing PM and MM features;

> 2) feature_set_name is a string containing the feature positions. If  
> one feature maps to position 123 and 456, feature_set_name will be  
> "123;456".
I see. So, just out of curiosity, how would you interpret these  
numbers (and indeed just the 'position' column when its singular) when  
the value of cdf$chromosome at that same index is <NA>?
> I'm far from claiming that this is the best storage system, but was  
> sufficient for an application we had a while ago.
> Anyways, I'm trying to move the creation of the PDInfo packages to  
> the pdInfoBuilder package, which uses SQL db to store these tables.
> If you're willing to give that a try, your comments and suggestion  
> are also very welcome.
As I come to better grips with how I'll be using the data for my  
analysis, I'll be happy to provide any feedback.

Erm, wait. Are you suggesting I use the pdInfoBuilder package to work  
with the tiling array? I looked at it briefly after reading somewhere  
that the functionality of the makePlatformDesign package will be moved  
there. The vignette for the pdInfoBuilder package requires that I  
already have some CDF file in order to play along, so I figured it  
wasn't for me and moved on for now (since my goal was to build the cdf  

I'll be happy to help you test the PDInfo packages and provide  
feedback, but it just wasn't clear to me that it did what I needed.



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