Auburn et al. SimArray: a user-friendly and user-configurable microarray design tool. BMC Bioinformatics 2006
Spatial bias heat maps
Spatial variation is observed even in the best laboratories [1-5]. Spatial bias can be
plotted in form of heat maps. The following heat maps were selected at random, and
show six dual-channel microarrays. The microarrays were printed and hybridised
according to the protocols given by the UK Drosophila microarray facility web site
[6]. The x/y-coordinates represent location on the microarray, whilst the colouring
and contours indicate the difference between the Cy5 and Cy3 channels. These six
examples show that spot location has a direct impact on the measured differential
gene expression ratios and hence supports the need for randomisation of the spot
layout to facilitate correction of spatial biases by normalisation [7-11].
-1-
Auburn et al. SimArray: a user-friendly and user-configurable microarray design tool. BMC Bioinformatics 2006
First example
Two patches of high gene expression ratios towards the centre of the array and
decreased ratios towards the edges, especially the right edge. The top and bottom are
roughly equivalent to the central region.
-2-
Auburn et al. SimArray: a user-friendly and user-configurable microarray design tool. BMC Bioinformatics 2006
Second example
Gradual increase in the measured gene expression ratios from bottom-to-top. The rate
of increase varies between the left and right, leading to a second gradient running
across the centre of the array from right-to-left.
-3-
Auburn et al. SimArray: a user-friendly and user-configurable microarray design tool. BMC Bioinformatics 2006
Third example
Low gene expression ratios at the centre, top and bottom of the array. Higher ratios
towards the left and right edges.
-4-
Auburn et al. SimArray: a user-friendly and user-configurable microarray design tool. BMC Bioinformatics 2006
Fourth example
Low ratios at the left and right edges that appear to increase towards the centre and
then again at the top of the microarray.
-5-
Auburn et al. SimArray: a user-friendly and user-configurable microarray design tool. BMC Bioinformatics 2006
Fifth example
High ratios at the bottom and top-left corner of the array, low ratios for one patch on
the left edge and the entire top-right corner.
-6-
Auburn et al. SimArray: a user-friendly and user-configurable microarray design tool. BMC Bioinformatics 2006
Sixth example
Reasonably even ratios across most of the microarray, but with slightly higher ratios
in the top-left corner.
-7-
Auburn et al. SimArray: a user-friendly and user-configurable microarray design tool. BMC Bioinformatics 2006
References
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