[BioC] beadarray package: problem with bead level data

[J.delasHeras at ed.ac.uk]

Quoting Krys Kelly <kak28 at cam.ac.uk>:

>
> I am having a problem with bead level data.
>
> I have .txt files containing over 900,000 lines with four columns: Code,
> Grn, GrnX and GrnY.
>
> The image files are .jpg rather than .tif. I have converted the .jpg images
> to .tif using Adobe Photoshop (trying several of the conversion options).
> They always look like a beautiful starry night sky, which I think is what is
> expected.
>
> However, the data in the beadarray object is not what I expected.  In G
> there are a lot of negative and zero values and all the Gb values are zero.
>
> On Wednesday, I downloaded the latest version of R, beadarray and the
> packages it depends on (see sessionInfo below).
>
> Is the problem with my .tif files, or is there a problem of incompatibility
> with the new version of R and the dependencies, or something else?
>
> Thanks for any light you can shed.
>
> Krys


Just a quick comment...

you are converting a jpeg to a tiff, for your quantitation, right?

is the jpeg 16-bit?

Jpegs are *usually* 8-bit, and I'd be surprised if yours is 16-bit,  
but they can be. If it's 8-bit, you're only getting 256 different  
intensities (2^8) rather than 65536 (2^16)... so I wonder if this may  
explain what you're seeing (you'd essentially get what looks like an  
extremely weak hyb, if the software reading the raw data expects a  
range between 1-65536 but the maximum is 256).

I am not familiar at all with beadarray, but your conversion concerns  
me. You'd better check that first.

Jose


-- 
Dr. Jose I. de las Heras                      Email: J.delasHeras at ed.ac.uk
The Wellcome Trust Centre for Cell Biology    Phone: +44 (0)131 6513374
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