Question: A weird PCA result using a local Galaxy
gravatar for Gary
5 weeks ago by
Taiwan/Taichung/China Medical University Hospital
Gary450 wrote:


We use a local Galaxy to run PCA (principal component analysis) based on six mouse RNA-Seq data. However, our result is weird: (1) PC1 can explain nearly all variation (94.5%); (2) All six samples on the 0.4 of PC1. Could you help us? Many thanks.



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ADD COMMENTlink modified 5 weeks ago by Devon Ryan88k • written 5 weeks ago by Gary450

If almost all the variance is explained by the first PC, it means that the variables are collinear, i.e. they can all be expressed as a linear transformation of one of them. If this is not what you expect, check that the data is really what it should be.

ADD REPLYlink written 5 weeks ago by Jean-Karim Heriche18k

This is from plotPCA in deepTools, which unfortunately defaults to not transposing the matrix before computing the PCA (I assume it was done this way originally since the PCA() function in matplotlib doesn't accept matrices with more columns than rows). So in this case the results just indicate that "genes are quite variable, but similar between samples", which is OK for basic QC but usually not what people actually care to look at in a PCA.

ADD REPLYlink written 5 weeks ago by Devon Ryan88k

Many thanks to your super professional answer.

ADD REPLYlink written 5 weeks ago by Gary450
gravatar for Devon Ryan
5 weeks ago by
Devon Ryan88k
Freiburg, Germany
Devon Ryan88k wrote:

Make sure to set Transpose Matrix to Yes (it's under Show advanced options). The resulting plot will be much more useful (I wish I'd just made that the default).

ADD COMMENTlink written 5 weeks ago by Devon Ryan88k
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