[BioC] Re: Bioconductor and Spot question

[Jeff Gentry]

(pardon the top posting here)
Dick ...

I'm forwarding this to the Bioconductor mailing list as I honestly don't
know the answer to this question, but am sure someone here will. :)

-Jeff

On Fri, 24 May 2002, Dick Beyer wrote:

> I am trying out Spot and the Bioconductor package.  I like it very much.  However, I am worried about the processing of the tiff files by Spot.  Do you know if Spot can handle the GEL files that are output by the Molecular Dynamics scanner?  These are special format tiff images with the following characteristics:
> 
> Gel files are special format 16 bit TIFF files. Each color is saved as a
> separate 16 bit grey scale image.  In addition, due to the large dynamic
> range of the scanner (about 6-7 logs) and the limited dynamic range of a 16
> bit image (0-65,000), the intensity data is saved as the square root of the
> intensity divided by a scaling factor.  The single color images can be
> viewed in some imaging software (not all image display software allows the
> display of 16 bit TIFF images) as grey scale images.  However, unless the
> software was written to understand the MD format (e.g. Was written for
> scientific applications) it is unlikely that the relative intensity values
> displayed by the software will be the correct values.
> 
> If you have any information about these tiff files and Spot, I would greatly appreciate your sharing that with me.
> 
> Thanks,
> Dick
> 
> *******************************************************************************
> Richard P. Beyer, Ph.D.	University of Washington
> Tel.:(206) 616 7378	Environmental Health, Box 354695
> Fax: (206) 685 4696	4225 Roosevelt Way NE, # 100
> 			Seattle, WA 98105-6099
> *******************************************************************************
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