Hi Christian,

There isn't an easy way to plot the intensities of the outlier beads only - I'm not sure that such a plot would be very informative.
The function plotBeadLocations() may be worth a try though.  This function plots the location of outliers, or other beads of interest on the array surface, which can reveal spatial biases (ideally beads/outliers should be randomly distributed across the array).  Check out its help page or the example in the Bioc07 tutorial at http://www.bioconductor.org/workshops/2007/BioC2007/labs/beadarray/ (take the 'Lab.pdf' link and see exercise 6).  Looking at imageplots alongside a plot of the location of the outliers can be informative.  You would hope to see areas with unusual signal biases flagged as outliers and removed by Illumina's standard summarisation method.

Best wishes,

Matt

-----Original Message-----
From: bioconductor-bounces@stat.math.ethz.ch on behalf of Christian Kohler
Sent: Fri 5/2/2008 5:36 PM
To: BioC
Subject: [BioC] beadarray: how to apply imageplot() on BLData-outliers ?
 
Dear all,

after unsuccessfully spending some hours on the following problem, I
would like to ask for your help.

My current situation:
I have read in several illumina tif-files into one BLData object; then I
applied findAllOutliers() to every array within this object.
The result looks like this:

>List of 21
 $ : int [1:45382] 34 47 52 55 123 125 131 141 153 159 ...
 $ : int [1:50858] 4 10 28 32 34 43 61 79 114 115 ...
 $ : int [1:49176] 1 7 19 32 46 49 55 68 69 75 ...
.
.
.
.
The above list contains the index of each outlier of each array.

My problem:
Is it possible to apply the imageplot()-function to a subset of the
BLData object above?
I mean, imageplot() takes a whole BLData object (including outliers) but
I would like to only draw the intensity (and therefore the location) of
the outliers. (question to experts: does a plot like this make sense
anyway?)
How can I extract the outlier-information from BLData and store the
'modified' information in another BLData object?


I am very happy for any suggestion.

Best,
Christian


-- 

Christian Kohler
Institute of Functional Genomics
Computational Diagnostics
University of Regensburg (BioPark I)
D-93147 Regensburg (Germany)

Tel. +49 941 943 5055
Fax  +49 941 943 5020
christian.kohler@klinik.uni-regensburg.de

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