Entering edit mode
> Date: Fri, 25 Feb 2005 17:16:43 -0500
> From: Pita <pwilkinson_m@xbioinformatics.org>
> Subject: mean vs median of pixel values within spot mask wasRe:
[BioC]
> something weird with read.maimages and .gpr files
> To: bioconductor@stat.math.ethz.ch
> Cc: bioconductor@stat.math.ethz.ch
>
> It seems that I answered my own question ....
>
> There was a typo that was entered into the Genepix software so the
output
> would not parse. Limmas read.maimages looks specifically for the
F532 Mean
> for the R channel, instead F594 Mean was written
>
> Since it is the case that the Mean of the pixels in the pot mask are
used
> in limma as default: are they any arguments for using the mean
values over
> the median values?
Limma uses the mean of the foreground pixels according to the
intuitive argument given in
Smyth, G. K., Yang, Y.-H., Speed, T. P. (2003). Statistical issues in
microarray data analysis.
Methods in Molecular Biology 224, 111-136.
http://www.statsci.org/pubs/mareview.pdf
i.e., because the mean is proportion to the total number of molecules
binding.
Limma uses the median of the background because (i) here the aim is to
measure the ambient level,
not the total binding, and (ii) because it is desirable for noise
reduction for the background to
be slightly lower than foreground, and the median of a right skew
distribution is lower than the
mean.
> Would the assumption here be that the spot morphology
> must be impeccable?
I have not yet seen any compelling evidence that the median foreground
is more reliable or more
tolerant of poor spot morphology than the median foreground in this
context. If you can cite such
evidence, it would a useful contribution to the debate.
Gordon
> Peter
