Hi Alan,

That's correct.  The Grn values in the .txt file have already undergone a
background subtraction step. As you say, beadarray allows you to calculate
the foreground and background values independently and manipulate them as
you like, but this does require the tif images.

Specific details of the default Illumina intensity calculation can be found
in the Oliphant et al, 2002 and Smith et al 2010.

I hope that helps,

Mike Smith

On Wed, Aug 3, 2011 at 10:49 PM, Mueller, Alan
<A.J.Mueller@liverpool.ac.uk>wrote:

> Hi,
>
> I am approaching beadarray for the first time and I have a query about the
> bead-level data that I have received.  From what I read four columns are
> expected in the .txt files (Code, Grn, GnrX, GnrY).  I want to clarify that
> the column GrnB (as per Dunning, 2011) can only be arise from analysis of
> .tif files, and that 'readIllumina' will extract background corrected
> intensities from the .txt files.  As yet the .tif files have not been made
> available to me.
>
> Many thanks in advance
>
> Alan
>
>
>
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-- 
Mike Smith
PhD Student
Computational Biology Group
Cambridge University

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