Scaling the observations

1 GPMelt does not require Fold Changed data anymore

For users already familiar with TPP-TR analysis, you may have been used to work with Fold changes, i.e. the preprocessed data are scaled with Fold Change (FC), such that the scaled observations would always start at one (requirement linked to the sigmoid fit).

The Fold Change scaling of the observations consists in scaling intensities of a replicate by the intensity at the lowest measured temperature.

We explain in Video 1 why we need to scale the raw observations, and we present different scaling methods discussed in GPMelt (Le Sueur, Rattray, and Savitski 2024).

Video 1: Why and how to scale raw intensities ?

References

Le Sueur, Cecile, Magnus Rattray, and Mikhail Savitski. 2024. “GPMelt: A Hierarchical Gaussian Process Framework to Explore the Dark Meltome of Thermal Proteome Profiling Experiments.” PLOS Computational Biology 20 (9): e1011632.