[BioC] LimmaGUI Spot Quality

Gordon Smyth smyth at wehi.edu.au
Sat Jul 3 00:33:24 CEST 2004

At 11:13 PM 2/07/2004, Elizabeth Brooke-Powell wrote:
>Hi James,
>The confidence values are give in numbers as decimals with 1 = 100%
>confident (e.g. confidence value = 0.78) this is a value determined using
>Bayesian statistics and is a measure of how confident the package is that
>the spot it found is real. The package itself (BlueFuse only currently
>available in the UK) uses a Bayesian model to iteratively find spots
>looking. I don't know much more as it's protected, and I'm a biologist.
>Basically I am asking if the model can take account of these numbers and
>adjust the model appropriately.

The answer is yes, in principle, but not without knowing how BlueFuse's 
"confidence value" is defined and what it means. Is the confidence value a 
probability? If so, of what? Is it a weight or an inverse variance? If so, 
of what? How does "confidence value" interact with the FLAG column included 
in BlueFuse output? You might not be able to answer these questions 
yourself but the BlueFuse developers can. I have not been able to find 
technical information on the BlueFuse www site sufficient to answer these 

Without knowing anything further, I would be inclined to treat the 
"confidence values" directly as weights in limma normalization and 
differential expression analyses. This is simple to do in principle, but it 
is not clear now to read the data in. The BlueFuse format is different to 
that of other two color image analysis programs. Is the RATIO column in the 
BlueFuse output the same as AMPCH1 divided by AMPCH2? If not, what are 
AMPCH1 and AMPCH2? We need to know this.


>  I am not sure in this case that pretending
>to have GenePix will work as the numbers are not a simple 0 or 1 (good or
>bad). If I was to try this, do I need to format the txt file of data to look
>like a GenePix file?
>Thanks for you help,

Dr Gordon K Smyth, Senior Research Scientist, Bioinformatics,
Walter and Eliza Hall Institute of Medical Research,
1G Royal Parade, Parkville, Vic 3050, Australia
Tel: (03) 9345 2326, Fax (03) 9347 0852,
Email: smyth at wehi.edu.au, www: http://www.statsci.org

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