AptMidas: Graphical interface to APT midas

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 midas program for detection of alternative splicing detection implemented in the Affymetrix APT tools

Usage

AptMidas()

Note

For more information see Affymetrix Alternative Transcript Analysis Methods for Exon Arrays whitepaper. Before using MiDAS is strongly recomanded to filter out gene level probe sets with low intensity values to avoid searching alternative splicing for probe sets which are not expressed. This can be done using filtering method implemented in oneChannelGUI which define a background intensity threshold on the basis of the intron exon signals of a set of housekeeping genes present in the exon arrays. However it is also possible to use a filter based on the dabg p-value calculated using Affymetrix APT tools. This function will also calculate Splice Index

Author(s)

Raffaele A Calogero

See Also

erankProdAltSpl

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