omicsplayground
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Review imputation for outliers methods
https://github.com/bigomics/omicsplayground/pull/1221/files
So for playbase::detectOutlierSamples
we do not need to impute. for singular value decomposition yes in this case.
Also, for corX we could use: corX=cor(t(scaledX), use="pairwise.complete.obs")
which uses all complete cases with no NA.
Correlation here is at sample level (for outlier detection) for at feature level.
We could also remove results_outlier_methods
entirely and handle differently. Let's focus on this later.
Thanks Xavi! I forgot to add that we had in use playbse::is.xxl(), however that was in imputed() and was for features not for samples in order to cover both. That was disabled as part of MPoC.