Description Usage Arguments Value Author(s) Examples
This function preprocesses an AffyBatch, ExonFeatureSet, or GeneFeatureSet object using the fRMA method.
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object |
an AffyBatch, ExonFeatureSet, or GeneFeatureSet |
background |
type of background correction to perform: either "none" or "rma". |
normalize |
type of normalization to perform: either "none" or "quantile". |
summarize |
type of summarization to perform: one of "median\_polish", "average", "median", "weighted\_average", "robust\_weighted\_average", "random\_effect". |
target |
summarization level for exon and gene arrays. Must be one of: probeset, core, full (exon only), extended (exon only). |
input.vecs |
a list of vectors to be used in preprocessing. If NULL, the correct package with pre-made vectors is loaded if it has been installed. These packages are of the form: <platform>frmavecs. |
output.param |
a vector of output elements to return. By default only the expression values and standard errors (if applicable) are returned. Additional options are: "residuals", "weights", "random_effects" |
verbose |
logical value. If TRUE then some messages are displayed while the function runs. |
The function returns an ExpressionSet if output.param=NULL or an frmaExpressionSet otherwise.
Matthew N. McCall
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