agilent.miRNA.preprocess.GX10: Preprocess Agilent miRNA data Preprocess raw Agilent data,...
In drmjc/microarrays: A collection of microarray and genomic helper code.

Description Usage Arguments Value Author(s)

Preprocess Agilent miRNA data Preprocess raw Agilent data, then threshold it to a minimum value, log transform, normalise each array such that the 75th percentile is 0.0, throw away miRs from other species, and keep those that are detected at least min.Pcount times. Optionally makes a 2x2 portrait layout plot @ each step. This is the default procedure by GeneSpring GX 10 (not sure about newer versions)

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  agilent.miRNA.preprocess.GX10(data, min.thresh = 1,
    percentile = 0.75, min.Pcount = 1, species = "mmu",
    plot = FALSE, do.par = TRUE)

`data`	a `list` of imported Agilent data. see `import.agilent`
`min.thresh`	if any values are < this value, then truncate them to this value. see `agilent.miRNA.threshold.GX10`
`percentile`	The percentile to perform percentile-shift normalization. See `agilent.miRNA.normalise.GX10`
`min.Pcount`	integer exclude genes detected in fewer than `min.Pcount` samples. see `agilent.miRNA.filter.GX10`
`species`	the 3 letter code for which species of miRNA's to include. see `agilent.miRNA.filter.GX10`
`plot`	logical: add boxplots of data during the transformation process
`do.par`	logical: configure the plotting device settings?