Description Usage Arguments Details Value Author(s)
View source: R/GEX_process_eset.R
Normalisation, transformation and/or probe quality filtering of expression data.
1 | process_eset(eset, method_norm = "quantile", transform = "none")
|
eset |
ExpressionSet or ExpressionSetIllumina |
method_norm |
character with normalisation method. Options are "quantile", "qspline", "vsn", "rankInvariant", "median" and "none" |
transform |
character with data transformation method. Options are "none", "log2", "neqc", "rsn" and "vst". |
Expression data is normalised and/or transformed by algorithms dedicated in 'method_norm' and/or 'transform'.
If a column PROBEQUALITY
is available within the feature data as for Illumina expression arrays,
probes assigned a ‘Bad’ or ‘No match’ quality score after normalisiation are removed from the dataset.
Lastly, if the input object is of class ExpressionSetIllumina
, it is changed to ExpressionSet
to avoid later incompabilities with the 'limma'-package.
processed ExpressionSet object
Frank Ruehle
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.