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Topic: Cloud plot: upregulated vs. downregulated (Read 3170 times) previous topic - next topic

Cloud plot: upregulated vs. downregulated

Hello,

I have just discovered that the Cloud Plots in XCMS Online are a fantastic way to explore features of interest in a dataset. However, the terminology of 'upregulated' and 'downregulated' is potentially a bit confusing. Clearly I have uploaded two datasets which are entered into the online tool as 'Dataset 1' and 'Dataset 2'. Based on the box and whisker plots, 'upregulated' seems to be higher in dataset 2. However, I could not find any documentation actually stating this. I had actually expected upregulated to be higher in dataset 1.

I wonder if the phrasing in the Cloud Plot could be more broadly described in the figures as "higher peak heights in dataset 1 (or 2)"'? My reasoning is as follows. For an experiment in the lab, I the datasets are presumably  (1) one set of experimentally altered samples compared to (2) an un-manipulated control. However, for a set of field samples, the description does not always fit into experiment vs. control. For example, I could have fish from Lake A compared to fish from Lake B. Neither one is a control per se, but there are differences across each lake.

This is not really a question per se since I mostly wanted to suggested a slightly different phrasing for the cloud plots. However, if I am wrong about 'upregulated' meaning that peak heights are higher in dataset 2 I would like to know.

Thanks,
Krista