Many thanks for this further info.
I am taking from your remarks on AmpCh1 and AmpCh2 that we can read
into R and ignore the various ratio columns as these can be re-
from AmpCh1 and AmpCh2.
You are describing the "confidence estimate" as as an intuitive
understand the need for something intuitive. Unfortunately for use in
numerical calculations we need a measure which is quantitatively
something, e.g., is quantitatively related to the estimated variance
log-ratio is some way.
At 12:45 AM 4/07/2004, Graham Snudden wrote:
>To pick up the points raised in the mail below.
>1. The confidence estimate to which Liz refers is derived from the
>distributions returned by the Bayesian framework that we are using to
>estimate the biological signal at each spot location. The underlying
>framework is relatively complex and provides a number of metrics
>the signal in each channel. In order to simplify these metrics and
>intuitive to the end user (biologists) we generate a single
>estimate. This estimate reflects the distribution of the ratio, i.e.
>confident are we in the value calculated for the ratio. In most cases
>tight signal distribution in each channel will lead to a high
>however it is possible that a very broad distribution in one channel
>weak, or saturated, spot - and a very tight distribution in the other
>also lead to a low confidence. A positive control, with near zero
>one channel, will therefore return a low confidence reflecting the
>degree of ambiguity in the actual value returned for the ratio. The
>associated confidence flag is derived from the confidence estimate by
>simple lookup table which is under user control. This is described on
>website if you follow the 'colour coded confidence flags' link on the
>product page; http://www.cambridgebluegnome.com/products/index.htm
>2. The AmpCh1 and AmpCh2 columns return our estimate of the total
>each channel. Clearly as we are not thresholding out an area of
>have no concept of mean or median pixel intensity neither do we need
>perform background subtraction as the amount of signal per spot is
>by the underlying models independent of any noise processes. The
>the ratio between the two channels.
>If you need additional technical information I could put you in touch
>our academic founders out of the signal processing lab here in
>Clearly we are using the very different approach to more traditional
>threshold/template based solutions however our experience is that the
>Bayesian approach offers significant advantages in terms of
>automation, detection, accuracy and, as described above, confidence
>From: Gordon Smyth [mailto:email@example.com]
>Sent: 02 July 2004 23:33
>To: Elizabeth Brooke-Powell
>Cc: 'James Wettenhall'; firstname.lastname@example.org;
>Subject: RE: [BioC] LimmaGUI Spot Quality
>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
> >Bayesian statistics and is a measure of how confident the package
> >the spot it found is real. The package itself (BlueFuse only
> >available in the UK) uses a Bayesian model to iteratively find
> >looking. I don't know much more as it's protected, and I'm a
> >Basically I am asking if the model can take account of these
> >adjust the model appropriately.
>The answer is yes, in principle, but not without knowing how
>"confidence value" is defined and what it means. Is the confidence
>probability? If so, of what? Is it a weight or an inverse variance?
>of what? How does "confidence value" interact with the FLAG column
>in BlueFuse output? You might not be able to answer these questions
>yourself but the BlueFuse developers can. I have not been able to
>technical information on the BlueFuse www site sufficient to answer
>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,
>is not clear now to read the data in. The BlueFuse format is
>that of other two color image analysis programs. Is the RATIO column
>BlueFuse output the same as AMPCH1 divided by AMPCH2? If not, what
>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
> >bad). If I was to try this, do I need to format the txt file of
> >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: email@example.com, www: http://www.statsci.org