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)