[BioC] Affy RNA digestion plots (fwd)

Leslie Cope cope at mts.jhu.edu
Mon Mar 10 11:39:52 MET 2003

> From: Matt Wayland <mwayland at hgmp.mrc.ac.uk>
> To: Bioconductor at 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.

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