[Bioperl-l] Bio::Expression & Re: ReseqChip, module/package name

Chris Fields cjfields at uiuc.edu
Fri Aug 24 13:20:16 EDT 2007


On Aug 24, 2007, at 11:32 AM, marian.thieme at arcor.de wrote:

>> ...
> The problem I see, with Bio::Expression, is that Resequencing chips  
> are not belongs to Expression chips.
> (Expression chips are designed to hybridisize RNA strands and hence  
> measure RNA expression levels, on the other hand a resequencing  
> chip is based on DNA, also the design and the probe length is quite  
> different). So, from my point of view it make sence to differ  
> between dna and rna chips, at least.

Then maybe the more generic Bio::Microarray namespace is the way to  
go, with the module name Bio::Microarray::Tools:: MitoChip.  If  
needed other tools can be added as needed.

>> Also, your module deals with doing one specific thing (extraction and
>> incorporation of information about redundant fragments) for the Affy
>> MitoChip.  It might be worth genericizing the class a bit so that you
>> can add new parser or analysis methods w/o having to define new
>> classes to deal with the same Mitochip data.
>
> OK, need to think about that.

It all depends on how much you intend to contribute; if you plan on  
adding to it over time we can talk about starting up a developer  
account.

>> Mail list: The mail list subscription page (http://bioperl.org/
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>>
> cleared
>
>> Bugzilla: if you are logged into Bugzilla under your old email, there
>> is an option at the bottom of the page (Edit : Prefs) where you can
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>>
> unfortunatly I dont recieve a mail to confirm the change. did try  
> that twice..
>
>
> Marian

I tested it out and received the email at both addresses (as it  
states).  If you respond to either email it should implement the  
change in three days time.  If it doesn't you can email support at  
open.bio.org to see if there is a problem.

chris


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