[Bioc-devel] suggestions for minfi

[Maarten van Iterson]

Dear developers of minfi,

I have a few suggestions for minfi:

1) In a few analyses with >500 samples we noticed that often the number of
PCs should be larger than the default of 2 for functional normalization.
Now we extract some code from minfi, not exported, using the triple colon
operator, to create such plots. It would be nice if there was a function to
plot the variance explained of the first few pc of the control matrix. For
example, something along the lines of:

controlMatrix <- .buildControlMatrix450k(.extractFromRGSet450k(RGset))
pc <- prcomp(controlMatrix)
##set nmax e.g. to 10 or so
nmax <- ifelse(nmax > nrow(controlMatrix), nrow(controlMatrix), nmax)
barplot(summary(pc)$importance[2,1:nmax], ylab="Proportion of Variance")

and optionally return the pc-object e.g. to correlate with known covariates
for further inspection.

2) Add function argument na.rm=FALSE/TRUE to detectionP which should be
passed to  colMedians and colMads such that detectionP can handle NAs in
the Red and Green intensity matrices of an rgSet. If na.rm=TRUE some
detection P-values will be NA, if these were NA on the probe-level, but
this is we want. For example, we use this for some probe-level filtering
steps e.g. on the number of
beads minimally required.

3) Are there any plans to support reading idats-files in parallel using the
BiocParallel functionality? For example, read.450k.exp could easily be
parallelized and for the reduce step 'combine' from Biobase can be used.

If you wish I can share some code on these suggestions.

Kind regards,
Maarten

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