Table 2 Summary of results.

There is local discordance between the locations in the two channels from two-colour arrays

Between-channel differences in location can be compared to local median differences

If one channel is clearly wrong (from relative grid positions in that channel) then the bead-centre can be remapped from the other channel, else the bead should be dropped

Image cropping out part of the array section, so that values cannot be calculated

Bead-centre coordinates lie without the dimensions of an image, beads apparent on edge of image

Exclude beads with such coordinates

Any text editor can assess the coordinates, while beadarray contains code for the reading and plotting of images on a useful scale. beadarray allows for the masking of beads to be excluded in analyses.

Beads are mostly well-registered, but grid of bead-centres does not align with the image resulting in scrambling of bead-type data

Visual inspection of bead-centres over image. Without access to images, check that the segments have similar extreme x coordinates and that they are equally spaced along the y-axis

In extreme circumstances, bead IDs can be remapped, but usually segments/sections should be excluded

beadarray contains code for the reading and plotting of images, as well as the over-laying of bead-centres. beadarray allows for the masking of beads to be excluded in analyses. Scripts are provided for automatic re-mapping

Neighbouring beads of the same bead-type are a potential concern (albeit unsubstantiated)

Such pairs of beads can be identified and down-weighted or excluded

beadarray contains code for identifying the network neighbourhood. beadarray allows for the masking of beads to be excluded in analyses.

Beads neighbouring clusters of non-decoded beads are more likely to take extreme values

The presence of such clusters can be determined from the .locs file

Exclude/Down-weight beads in a zone about such clusters

beadarray allows for the masking of beads to be excluded in analyses.

Bright beads encroach on neighbours, raising their associated values

Visual inspection of the brightest beads

Bright beads can be identified (by intensity or size using EBImage) and their neighbours down-weighted or excluded

beadarray contains code for the reading and plotting of images, as well as code for identifying neighbours. beadarray allows for the masking of beads to be excluded in analyses.

Abnormally low pixels in the image distort background values and so final intensities

Pixels present with values noticeably lower than the mode

Exclude such pixels, or use a less-sensitive background calculation rule

beadarray contains code to read images, which allow for tests of the distribution of intensities within R. beadarray allows alternative background calculation rules

Multiple bead-centres map to the same location

Text files (or .locs files) can be scanned for neighbours that are unusually close

In two-colour arrays, it may be clear which is the correct bead-centre, else exclude both

Scripts provided to detect departure from predicted bead-centre.