The affy.tools node in SciCraft has the
following input arguments:
- FileNames: Names of the .CEL files to analyse
- Path: Path to directory of cell files.
- Normalisation: Text box containing the choice of which
normalisation method to use with the following three choices:
- MAS.5 (default)
- GCRMA
- RMA
- Filtering: Text box containing which choices on how to filter the
genes using affymetrix present absent calls, with the following
three choices:
- none
- Remove all absent genes
- Remove all absent or marginal genes
The output arguments from the node are:
- calls: Matrix containing the present and absent values for each gene
- Expr: Matrix containing the expression levels.
- genID: R object containing the Affymetrix Id's
for all genes.
- R.obj: R object containing the following elements:
- exprs: Matrix containing the normalised expression
levels. The columns represent the patients or cases and the row
represent the genes.
- se.exprs: Matrix containing the estimated standard
error for the estimated expression levels.
- phenoData: R object containing the patient (or case)
level data.
- annotation: String identifying the annotation
- s.expr: Matrix containing the standard error of the
expression values.
Bjørn Kåre Alsberg
2006-04-06