Effect Size(s) for Power Calculations

I’m trying to conduct a power calculation using metabolomics and lipidomics data. I’m trying to determine the estimated effect sizes using the power calculation module. In the report, it mentions that the density of estimated effect sizes is shown - but there is no figure that I can see. How can I view or see this data?

Please use the web interface as your reference point, as the PDF report will be deprecated gradually. For your question, the module is designed for estimating the sample size based on a pilot data.

Dr. Xia,

Thank you.

A couple of clarifying questions. What effect size statistic is used for the pilot data? is it comparing log fold change? Means? Medians? Geometric means? Something else entirely? I assume that there is a different effect size gathered for each individual metabolic compound and that the range (along with the FDR and sample size) allow for the creation of the predicted power curve? I’ve tried looking at this a bit in the R code but I can’t seem to determine whether the above is true or not?

I’m a big fan of metaboanalyst and your work. Thanks for all that you do!!


Jon Reiss MD
Stanford University

Yes, you are right. I believe it is the average effect sizes of individual features used here. I will save this table so you will see it in the download page. The feature will be available some time next week, as we are in the middle of a major update V 6.0.

Revisiting this query from a few weeks ago. Do you know which effect size tool or calculation is used? Is there a way to find out and see a table of it effect sizes ranges for each feature? I don’t see it either within the URL or on the download pdf.

The histogram/density curve is provided to show the distribution of the effect size as a diagnostic plot. You can find this figure “effect_size_distribution_dpi96.png” in the download result table.

There are many features that could be enhanced in this direction, but left aside due to limited resources. We now try to address the issue by offering pro support to subscribed users.

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