ArrayPipe Online Documentation

Sample Analysis

Settings Check

To make sure that the data settings are correct it is advisable to always start with some simple chip visualizations. In the ACTION SETUP section define the following steps:

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After clicking on the red 'Do it!' button the data processing is started. A temporary message comes up and refreshes until the final results are available:

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The patterns visible from the background intensities span across subgrid boundaries and form a coherent picture. This confirms that the grid layout and data organization has been specified properly. With incorrect data settings, e.g. 'by-row' file organization rather than 'by-subgrid' the chip image would look like this:

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This effect of repeated patterns within subgrids but no connection between them is a good indication for wrong file organization settings.

Based on the frequency of their occurrence the following spots were flagged as markers:

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These show up as magenta coloured fields on the next chip visualization:

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Shown are the two channels from the first data file. Please note that the images are turned onto their side by default to use space more efficiently with larger chips. The markers are located along the top row of each subgrid, which can be easily verified from the GAL file accompanying this data set. This provides further confirmation that our data settings are correct!

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last modified $Date: 2007/08/27 14:02:03 $
for questions or remarks e-mail karsten_hokamp@sfu.ca.