[BioC] Reading Imagene files with read.imagene in limma

Gordon Smyth smyth at wehi.edu.au
Tue Jun 8 10:50:25 CEST 2004

At 06:04 PM 8/06/2004, STKH (Steen Krogsgaard) wrote:
>notation. Besides, I still would like to have the original flag values
>stored in the RGList object so that I can re-do the filtering later or
>plot the flagges spots or whatever.

limma doesn't include the flag values themselves in the output object, 
because the different image analysis programs have quite different 
treatments of this concept. It is desirable to produce a data object all 
the components of which have meanings not dependent on the specific image 
analysis program used. Moreover, there may not be a single flag column from 
which the quality weights are computed - the weights may depend on two or 
more columns. Therefore the approach has been taken to compute numeric 
weights directly within the read.maimages() function, but to provide the 
facility for users to define how these are computed.


>Thanks for all the feedback

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