Hi Jason,

Hope you don't mind but I'm replying on the Bioconductor mailing list 
as I think this might be a common question.

Illumina recently changed their policy so that bead level csv files 
(including bead coordinates) are easily available. Previously we 
obtained these files by sending the encrypted dmap files by FTP to 
Illumina and they used some in-house application to de-crypt for us. 
The csv files can now be obtained using BeadScan versions 3.1 and above 
and have the IncludeXY parameter in the config file.

To my knowledge, these files can only be created when the arrays are 
scanned and cannot be retrieved later on. If you only have the TIFF 
images without the corresponding bead centre coordinates you will 
unfortunately not be able to do background correction or sharpening. I 
don't think that Illumina are planning to make their in-house 
application for de-crypting dmap files available. Unless of course 
enough people pressure them about it...

Hope this helps,

Mark


On 10 Jul 2006, at 15:08, Jason Affourtit wrote:

>
> Hello Mark,
>  
> I have recently been evaluating your beadarray R library and came up 
> with a question with which I was hoping you could help.  How does one 
> obtain the CSV file of bead locations/identities?  Forgive my 
> ignorance, but we have not yet received our Illumina platform and I am 
> unfamiliar with all of the output files created.  We had a pilot 
> experiment performed for us at Illumina and while we received the TIFF 
> files, we did not get the decoded bead locations (.dmap file?).  I was 
> told these .dmap files were available but that they are encrypted and 
> only for use with the BeadArray scanner.  At this point I’m unclear as 
> to how we can proceed with doing bead level analysis without 
> sharpening/background subtraction and would greatly appreciate your 
> assistance.  I saw a BioC list posting by you that suggested that 
> Illumina was reluctant to share these data.  Is the decoded 
> information unavailable?
>  
> Thank you very much,
> Jason
>  
>
> ===
> Jason Affourtit
> Senior Manager, Phenotyping Sciences
> The Jackson Laboratory
> 600 Main Street
> Bar Harbor, ME  04609
>
> Phone: 207-288-6703
> Fax:     207-288-6325
> Email:  jason.affourtit@jax.org
>
> "In the beginning the Universe was created. This made a lot of people 
> very angry and has been widely regarded as a bad move." -Douglas Adams
>
>  
>  
>

Mark Dunning
PhD Student
Computational Biology Group
Hutchison / MRC Research Centre
Department of Oncology
University of Cambridge
Hills Rd, Cambridge CB2 2XZ

Email  : md392@cam.ac.uk
Phone : +44 (0) 1223 763389

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