Which images should I use for spot detection?

When SameSpots detects the spots in your experiment, it does so by examining each of the images selected in the Detection Parameters window.

The Detection Parameters window

Often, it will make sense to examine all images when detecting spots; this helps to make sure all spots are detected, even when some spots are not present in all images. It is advisable to include at least one image from each experimental condition.

There will be situations, however, in which it is appropriate to exclude some of your images from the spot detection process. It's important to note that the resulting spot pattern will be applied to, and measured in, all images listed in the Detection Parameters dialog.

For example, if your experiment contains images from different capture techniques such as protein and phospo-stain, or protein and immuno-blots, it may be appropriate to use only the images from one capture process to generate the spot pattern:

Detecting on only immuno-blot images

Other situations in which you may want to exclude some images from the detection process include:

• In very large datasets, some images from each test condition can be excluded to avoid over-influencing the pattern of detected spots
• In cross-lab studies, you may want to detect spots in, and later compare against, images from only a single source e.g. a high-quality lab (you can also use SpotCheck to perform quality control)