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 >>> >>>_______________________________________________ >>>Bioconductor mailing list >>>Bioconductor at stat.math.ethz.ch >>>https://stat.ethz.ch/mailman/listinfo/bioconductor >>>Search the archives: http://news.gmane.org/ >>>gmane.science.biology.informatics.conductor >> >>_______________________________________________ >>Bioconductor mailing list >>Bioconductor at stat.math.ethz.ch >>https://stat.ethz.ch/mailman/listinfo/bioconductor >>Search the archives: http://news.gmane.org/ >>gmane.science.biology.informatics.conductor