How can I export my spot data?

Melanie allows you to export a table with all spot data, also called project data. You can use the exported file for further analysis of your experiment with third party software. To export your project data, click the Project icon at the top left of the screen and then choose Export > Data > Save to file. NOTES Data export is only available in certain workflow steps. For expression analysis: in the Review and Results steps. For coverage analysis: in […]

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How does spot quantification work in MelanieTM?

In the detection step, spots are detected on a fusion image (which is not displayed, but which is generated based on the images marked for inclusion). The resulting spot pattern is propagated to the individual images, taking into account the deformation calculated in the alignment. For each spot on an image, MelanieTM  then computes the following quantification measures, based on the calibrated pixel gray values: Area: The area of a spot is the surface delimited by the spot border, and is […]

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How does normalization work in MelanieTM?

Why is normalization needed? 2D gel electrophoresis experiments typically aim at comparing different samples in order to identify protein expression changes that are characteristic of those samples. Nevertheless, relevant expression changes are often obscured by systematic experimental variation such as: Differences in sample preparation (inconsistent amounts of starting material, variations in reagents or protocols, pipetting errors) Differences in sample loading (pipetting errors, sample loss during gel loading) Differences in staining/labeling (inconsistent staining times, differences in labeling efficiency between CyDyes) Differences in image […]

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