Hello everybody 

Can any one help me understand the MDS plot for  two groups of samples like control vs. treated we generate from edgeR or Deseq2.  I understand the figure as it separates the control from treated very well, but if we have the y-axis as the logFC, I don't get what the x-axis is? What is the x-axis in such 2D figure? 

Thanks

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, <a href="https://www.bioconductor.org/help/workflows/rnaseqGene/#mds-plot">RNA-seq workflow: gene-level exploratory analysis and differential expression</a>, 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 <a href="https://stat.ethz.ch/R-manual/R-devel/library/stats/html/cmdscale.html">cmdscale</a> *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:

 - https://www.biostars.org/p/280615/#280634
 - https://www.biostars.org/p/282685/#282691
 - https://www.biostars.org/p/271694/

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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)