[BioC] Affy's .DTT format?

[Kasper Daniel Hansen]

On May 22, 2006, at 8:56 AM, Jenny Drnevich wrote:

> Hi everyone,
>
> Our core facility was told by our Affy rep they should switch to  
> the .DTT
> flat archive file instead of the CAB format as the way to store  
> data and to
> disseminate it to researchers. However, this file format is basically
> useless right now without Affy's Data Transfer Tool and GCOS  
> software; to
> get the .CEL files, I had to use the Data Transfer Tool to import  
> the .DTT
> file into my local GCOS database, then use it again to export the  
> flat .CEL
> files.  I've talked with our core, and instead they are going to  
> give out
> the .CEL, .CHP and .DAT flat files, at least for now. I noticed  
> that Affy
> does have a DTT SDK, and wondered if anyone within Bioconductor was
> planning on/working on being to import data from the .DTT format?  
> I'm not
> sure what our rep was thinking, because I don't think any analysis  
> software
> out there can take .DTT files (yet?).

Hi Jenny

The SDK we are interfacing to in affxparser contains methods for  
parsing DTT files. I did not really know of this format until this  
morning, and I am still trying to figure out whether it really makes  
sense to support. Basically it seems like a way to bundle cel, chp  
and dat files, and stuff I have read on the Affy website seems to  
indicate that it primarily makes sense for people wanting to share  
_all_ data and subsequently use it in some of Affy's own software.  
Eg. they provide both "flat" cel files and dtt-bundled cel files for  
some of their SNP data. It also seems like there exists both a dtt  
format and a "flat" dtt format - whatever the difference is. I will  
try to investigate a bit (and if you hear something please write).

Adding support for the DTT file to affxparser would be "simple" but  
probably take considerable time since that part of the SDK depends on  
external libraries we would then have to figure out how to deploy  
etc. My first impression is that it is not worth the effort to do  
this (unless we are forced :)

My final verdict will depend on my investigation, and - of course -  
whether there is a large interest in this...

/Kasper

> Cheers,
> Jenny
>
> Jenny Drnevich, Ph.D.
>
> Functional Genomics Bioinformatics Specialist
> W.M. Keck Center for Comparative and Functional Genomics
> Roy J. Carver Biotechnology Center
> University of Illinois, Urbana-Champaign
>
> 330 ERML
> 1201 W. Gregory Dr.
> Urbana, IL 61801
> USA
>
> ph: 217-244-7355
> fax: 217-265-5066
> e-mail: drnevich at uiuc.edu
>
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