[BioC] Affy's .DTT format?

[Jenny Drnevich]

Hi Kasper,

Thanks for looking into this - I was indeed able to upzip the .DTT flat 
file into the separate .CEL, ,CHP, etc. flat files. The zipping doesn't 
actually compress the total size of the files, but I guess for storing and 
transferring files, it's easier to have just one for each array instead of 
4-5 files; the .DTT flat file can be made with or without the .DAT using 
the Data Transfer Tool, but obviously the size with the .DAT is >100MB 
compared to <15 MB without. Either way, a .jpg file of the array image is 
included, which is new (to me) & useful to check for gross array defects!

Thanks,
Jenny


At 12:27 AM 5/23/2006, Kasper Daniel Hansen wrote:

>On May 22, 2006, at 4:30 PM, Kasper Daniel Hansen wrote:
>
>>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...
>
>Some investigation and an email to devnet at affy uncovered that the big
>DTT bundle is in fact just a zip file containing EXP, CEL and CHP
>files for each array. There seems to be an extra base file containing
>the CDF file. DAT files are not included.
>
>The DTT format I was referring to is an XML based format describing
>some details about the experiment in a MAGEML (like) structure.
>
>So I will not do anything about adding parsing capability - just use
>your favorite zip program. It is not worth the time and effort to
>parse DTT files using the SDK.
>
>As a small curiosity, some of the DTT files for the 100k snp arrays
>available on Affy's site are corrupted - look at the 500k instead.
>
>/Kasper
>
>>/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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>>
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