[BioC] LimmaGUI Spot Quality

James Wettenhall wettenhall at wehi.edu.au
Fri Jul 2 15:02:08 CEST 2004

Hi Liz,

limmaGUI is not as flexible as limma when it comes to spot 
quality measures for "new spot finding packages".  Please tell 
us the column name(s) from your raw image-analysis results files 
which you want to use for assessing quality, and if you can 
explain what the quality indicator in this column means (e.g. 
high=good, low=bad, ...), that would be even better.

Try the limmaGUI spot-quality-weighting option for GenePix.  
(Even if you don't have any GenePix files, you can just 
pretend you do have GenePix files in order to see the 
spot-quality weighting dialog.)  You can give different weights 
to different GenePix flags (for "bad" spots or "not found" 
spots etc.)  Is this the sort of thing you are looking for?

The extra quality column(s) are read in when the raw data is 
read in, and then they are used to form weights in the 
normalization routines in limma.

?wtflags (not as flexible as the limmaGUI GenePix flags dialog)

at the R prompt for a bit more information.


On Fri, 2 Jul 2004, Elizabeth Brooke-Powell wrote:

> Hi there,
> I have a question about limmaGUI. How are spot quality measures used? I am
> wondering because I am using a new spot finding package that generates
> confidence values on a per spot basis. Can these be used when loading the
> data? How will they be used?
> Any help is much appreciated,
> Liz Brooke-Powell 
> Molteno Building
> Department of Pathology
> University of Cambridge
> Tennis Court Road
> Cambridge, CB2 1QP
> United Kingdom
> Website: http://www.path.cam.ac.uk/~toxo/
> Tel 01223 33 33 31(office) or 01223 33 33 29 (lab)
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James Wettenhall                                  Tel: (+61 3) 9345 2629
Division of Genetics and Bioinformatics           Fax: (+61 3) 9347 0852
The Walter & Eliza Hall Institute         E-mail: wettenhall at wehi.edu.au
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