I quite like the idea of the positive border elements plots in
affyQCReport. However, I have a few suggestions for improvements and
would like to know what people think, and also how to go about achieving
it.
 
1) I think the boxplots should use log2 intensities rather than raw
intensities.
2) The way that +ve/-ve border elements are identified in the code
essentially takes all the spots around the perimeter of the array - PM
and MM. Positive and Negative border elements for each side of the array
are identify from the border elements (which contain PM and MM probes)
which are greater than 1.2 or less than 0.8 times the mean respectively.
Since, the distribution of intensities for a particular border contains
both PM and MM probes, there will be a bi-modal distribution to
complicate things. It seems to me, that it might be better to have a PM
border elements and MM border elements plotted on a log2 scale.
Therefore, my question is:
 
How do I obtain the PM and MM probe intensities separately from an
AffyBatch object for the first and last rows and columns of an array?
i.e. I want 8 vectors containing intensities for the PM and MM probes
for each of the four sides of an array.
 
Thanks for any help/comments,
Nathan
 
-------------------------------------------------------------
Dr. Nathan S. Watson-Haigh        (publish under Haigh, N.S.)
OCE Post Doctoral Fellow
CSIRO Livestock Industries
J M Rendel Laboratory 
Rockhampton
QLD 4701                              Tel: +61 (0)7 4923 8121
Australia                             Fax: +61 (0)7 4923 8222
-------------------------------------------------------------


	[[alternative HTML version deleted]]

