preprocess_eset_workflow: Workflow function for converting an ExpressionSet into an...
In russHyde/miiq: Microarrays Are Awesome: Get Them Analysed HERE!

Workflow function for converting an ExpressionSet into an entrez.id annotated ExpressionSet that has been log transformed / quantile normalised and median-normalised. Probes that do not map to entrez.id are dropped by default. All annotation / filtering functions can be overridden

preprocess_eset_workflow(gset = NULL, entrezgene_db = NULL,
  eset_annot_fn = gld_fnDefault_esetAnnotation,
  keep_sample_fn = keep_all_samples,
  transform_and_filter_fn = gld_fnDefault_transformAndProbeFilter,
  keep_probe_fn = keep_all_probes)

`gset`	An ExpressionSet (must have genbank ids or swissprot ids or similar for default annotation function).
`entrezgene_db`	character or `OrgDb`. Which `AnnotationDbi` object to use in the eset annotation function.
`eset_annot_fn`	Function that annotates an input ExpressionSet and outputs an ExpressionSet.
`keep_sample_fn`	Function that returns integer indices of samples (cols) of the ExpressionSet that are to be kept.
`transform_and_filter_fn`	Function that applies various filtering / transformation steps to the values in the input ExpressionSet and returns an ExpressionSet
`keep_probe_fn`	Function that returns integer indices of probes (rows) of the ExpressionSet that are to be kept.