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

marian marian at arcor.de
Fri Aug 24 14:48:20 EDT 2007


Hilmar Lapp schrieb:
> On Aug 24, 2007, at 1:20 PM, Chris Fields 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.
>>
>>     
>
> Makes sense to me too. Presumably, regardless of DNA or RNA being  
> hybridized or length of probes, the data that comes out of them is  
> quite similar in a general nature (namely hybridization signals)?
>
> 	-hilmar
>   

Bio::Microarray::Tools::MitoChip would be OK to me. I merely meant, that it 
isnt an expression chip and you also wont/cant analyze expression data with 
the tool I am talking about.

Marian



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