Entering edit mode
Leslie Cope
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50
@leslie-cope-215
Last seen 10.3 years ago
> From: Matt Wayland <mwayland@hgmp.mrc.ac.uk>
> To: Bioconductor@stat.math.ethz.ch
> Subject: [BioC] Affy RNA digestion plots
> I have found the RNA digestion plots useful, but have
> been disappointed that no scale is provided on the ordinate axis
(mean
> intensity). To try to get round this problem I printed the
means.by.number
> data (see below) and plotted these values against position in
probeset using
> MS Excel. I was surprised to find that the graphs produced in MS
Excel had
> quite different profiles to those displayed in the RNA digestion
plots.
What is plotted is the same standardized data used to produce slopes.
First
overall chip mean is subtraced chipwise from all means.by.number.
Then
each of the means.by.number are divided by corresponding standard
errors.
Finally the values 1 to number of chips
are added chipwise to the plotted values, to stagger the lines and
make them
easier to see. There is no scale, because after this it would not be
helpful.
means.by.number and standard errors are made available partly so you
can look
at raw data. Future releases will include other plotting options.