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What does single channel microarray mean? When is it used? Thank you for your case in advance.

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@PlaysDice - please avoid answering questions in comments - see the meta discussion here for more background. Thanks. –  MattDMo Mar 27 at 21:57
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Single channel refers to the system used to detect the labelled probes. A single channel array, as shown in this slidedeck (slides 6-8) uses one type of molecule for detection. In the example, (slide 8) the optical label is phycoerythrin. Contrast that to a double channel array (e.g slide 7) that uses a "green" or "red" molecule used to label probes. Detecting two different labels requires two channels, one to detect red and one the the green. The key to using two (or more) labeling molecules is to ensure that your detection system can discriminate between the light spectrum emitted by each of the labels. Many modern microarray readers have designs that handle multiple labels.
When you see single channel results, they often have colors. The color is a pseudo color representation of the intensity of the emission of single-color label, which is due to how much probe has bound to the array at that spot.

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Adding to this: When using only one color to mark the sample, you can only use one sample (direct comparisions are not possible, since they can not be discriminated). The intensity of the signal here is used to measure the strength of expression, which can also cause some bias. –  Chris Mar 28 at 7:25
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