Re: question regarding Colocalization Threshold in Fiji - Coloc2

Posted by Robert Baer on Aug 01, 2011; 9:49pm
URL: http://imagej.273.s1.nabble.com/Re-question-regarding-Colocalization-Threshold-in-Fiji-Coloc2-tp3683647p3683650.html

-- snip --

> images for example one “positive” image where colocalization is
> expected/”visible” and one “negative” image with no colocalized signals.
> Then, I´ve tested the results with the Colocalization test plugin and all
> the p values were much lower than 0.

the coloc test plugin randomises the image many times then compares pearsons
r for each with the original.
we expect there to be lower pearsons r values than the real image pair when
there is true coloc,
but about the same if the apparent coloc is no better than random.

read the Costes 2004 paper to get a full explanation.

Can you send me the images for testing?
>
> Do you really mean negative or is this a mis-speak?  The theoretical range
> of p is 0 to 1.0

no, the range for Pearsons r is -1 to +1

OK, so the OP meant the correlation coefficient,  r,   and not probability,
p, as he stated "p-value".   In that case, I would agree that it was an
innocent mis-peak on the OP's part and not an algorithm issue.  Clearly, the
range for the correlation coefficient CAN BE -1 to 1, but NOT the range for
probability.