MissMethyl: Sample size and control probes
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@taub-margaret-5847
Last seen 3.4 years ago
United States

I was wondering if anyone was aware of any issue with running RUVfit (as part of the missMethyl package) when I have a large number of samples from my methylation experiment? I am working with a data set with 634 samples and 18 covariates, and I am getting the following error in the invvar function that is called by RUVinv: "In function invvar: The fourth-smallest eigenvalue is more than 10 times larger than the smallest eigenvalue.  This is not currently supported, and very likely means something is wrong (perhaps a dimension was removed during preprocessing?)."

I believe this is happening because three of the eigenvalues computed in the invvar function are 0, which I think is the result of the number of control probes (613) being less than the number of independent components of the design matrix (634-18=616). Has anyone come across this before? Do you have any suggestions for a work-around? If I remove some samples, I no longer get the error, but I would of course rather increase the number of control probes instead. I just want to do so in a way that makes sense and won't break the functionality of the method, if possible.

Thanks for any help you can give me, it is greatly appreciated!

Cheers,
Margaret

missmethyl RUV control probes • 346 views
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