agilent.miRNA.preprocess: Preprocess Agilent miRNA data. From a table of imported...
In drmjc/microarrays: A collection of microarray and genomic helper code.

Description Usage Arguments Value Author(s)

Preprocess Agilent miRNA data. From a table of imported Agilent data, add an offset, truncate, log-transform, normalize and plot a set of Agilent microarray files. This combines transform_Agilent_log, agilent.miRNA.normalise.GX10 or normalizeBetweenArrays, and agilent.miRNA.filter.GX10

  agilent.miRNA.preprocess(data, offset = 8,
    min.thresh = 1, percentile = 0.75, min.Pcount = 1,
    species = "mmu", plot = FALSE, do.par = TRUE,
    norm.method = c("percentile", "none", "scale", "quantile"))

`data`	a `list` of imported Agilent data. see `import.agilent`
`offset`	add an offset. see `transform_Agilent_log`
`min.thresh`	if any values are < this value, then truncate them to this value. see `transform_Agilent_log`
`percentile`	The percentile to perform percentile-shift normalization. only used if norm.method=="percentile", 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?
`norm.method`	The normalisation method to use. one of “percentile”, “none”, “scale”, “quantile”. If “percentile”, then make sure you set the `percentile` parameter appropriately. If “scale” or “quantile”, then the `normalizeBetweenArrays` from `limma` is used. If “none” then no normalisation is performed.