Hello, the y-axis in a MDS plot does *not* represent logFC, and neither does the x-axis.

Provided you have generated the plot according to the workflow, RNA-seq workflow: gene-level exploratory analysis and differential expression, on Bioconductor, your x- and y-axes will be representative of **Euclidean distances** between your samples. These Euclidean distances will be produced/repeated across multiple dimensions in different ways, but the standard way of representing MDS is to just plot the Euclidean distances from the first 2 dimensions, with x-axis being *Dimension 1* and y-axis being *Dimension 2*. The dimensions are ordered based on how well they fit your samples (for further reading, take a look at the cmdscale *Details* section.

MDS is commonly used in genetic studies to find relationships between samples based on genotype, but, as you can see, it's also used in RNA-seq. For information on a related method, i.e., principal components analysis, please see my threads here:

For what it's worth:

- A volcano plot represents logFC (x-axis) and negative log10 P- or
adjusted P-value (y-axis)
- A MA plot represents average expression (x-axis) and logFc (y-axis)