This function estimates the number of surrogate variables that should be included in a differential expression model. The default approach is based on a permutation procedure originally prooposed by Buja and Eyuboglu 1992. The function also provides an interface to the asymptotic approach proposed by Leek 2011 Biometrics.
1 2 |
dat |
The transformed data matrix with the variables in rows and samples in columns |
mod |
The model matrix being used to fit the data |
method |
One of "be" or "leek" as described in the details section |
vfilter |
You may choose to filter to the vfilter most variable rows before performing the analysis |
B |
The number of permutaitons to use if method = "be" |
seed |
Set a seed when using the permutation approach |
n.sv The number of surrogate variables to use in the sva software
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