Hi there,

I used the Genesis clustering software (https://genome.tugraz.at/genesisclient/genesisclient_description.shtml) to cluster genes ito their expression, but would like to move over to the same kind of thing, but in R. In genesis, you have the option to "Normalise" your expression data - there is no transparency about what this normalisation step means, but from the output I assume it scales the data in some way.

I would like to switch over to something in R, such as the TMixClust package to better control this normalisation business. In the documentation (https://docplayer.net/95195923-Clustering-time-series-gene-expression-data-with-tmixclust.html), it does not specify whether the timecourse data can be normalised or transformed in any way prior to loading into the TMixClust function, for example log values or log fold change values of FPKM/TPM.

Can one use scaled/log transformed/fold change data with TMixClust?

Thanks!