Description Usage Arguments Value Author(s) References See Also Examples
Selects the Least Variant Set of genes, accordingly to the chosen proportion of genes expected not to vary between arrays.
1 |
object |
an object of class RA or a matrix with residual standard errors and array effects. |
proportion |
the proportion below which genes are expected not to vary between samples. Default is set to 0.6. |
DF |
the degrees of freedom used for the bi-spline in the quantile regression. |
... |
|
a TRUE/FALSE vector with the seleted ID probes from the quantile regression.
Stefano Calza <calza@med.unibs.it>, Davide Valentini and Yudi Pawitan.
S. Calza et al. 'Normalization of oligonucleotide arrays based on the least variant set of genes' (2008, BMCBioinformatics).
lvs
, normalize.lvs
,
compute.RA
,RA-class
,
normalize.AffyBatch.lvs
1 2 3 4 5 6 7 8 9 10 | ## Not run:
# Starting from an Affibatch object called aBatch
data.RA <- compute.RA(aBatch)
lvs.id <- lvs.fit(data.RA, proportion=0.6)
lvs.prep <- expresso(aBatch, normalize=FALSE,
bgcorrect.method="mas",pmcorrect.method="mas",
summary.method="mas")
normalize.AffyBatch.lvs(lvs.prep,lvs.id=lvs.id)
## End(Not run)
|
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