erankProdAltSpl: Implementation of the Rank Product method for the detection...

In oneChannelGUI: A graphical interface designed to facilitate analysis of microarrays and miRNA/RNA-seq data on laptops

Description

This is a graphical interface to the RP function from RankProd package applied to detection of alternative splicing

Usage

erankProdAltSpl()

Details

Before using this method it is strongly suggested to perform a filter on the basis of DABG p-values using the filtering function available in the filtering menu. DABG values can be calculated if exon array probe set data are generated using the oneChannelGUI graphical implementation to APT tools. Affymetrix suggests to calculate probe set intensity at gene level using iterPlier and at exon level using plier. Subsequently SpliceIndex need to be calculated using the function available in the exon menu. Finally the Rank Product method could be applied exon by exon. For more details on the method see RankProd package. Selection of putative alternative splicing could be done using the filtering function available in the filtering menu of oneChannelGUI

Note

IMPORTANT we are still evaluating the efficacy of this method for detection of alternative splicing events. Use it being concious of this!

Author(s)

Raffaele A Calogero

See Also

inspecting.splice, spliceIndex

oneChannelGUI documentation built on Nov. 17, 2017, 11:02 a.m.