[Bioc-devel] Updates: arrayQuality

Paquet, Agnes apaquet at medsfgh.ucsf.edu
Sat Dec 10 01:48:31 CET 2005

Hi All,

arrayQuality now includes a new series of functions specifically
designed for MEEBO arrays, which provide a wide range of control
sequences, such as positive, negative, tiled and doping controls. The
main function in producing quality plots for MEEBO arrays is called
meeboQuality(); the results can be summarized in 3 categories:

1- A figure including several statistics and exploratory plots. It is
similar to the other diagnostic plots generated with other functions in
this package and will provide a quick graphical insight on the quality
of the array. 

2- QC on doping controls: these plots show the performance of the doping
controls that were added to the hybridization mix, and compare them to
expected results.

3- Mismatch and tiled controls plots: these plots are designed to show
the specificity of the MEEBO set and to examine the level of
amplification bias toward the 3' end of the transcripts. These plots can
be used as a MEEBO print-run QC rather than general hybridization
quality assessment.



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