AboutextendedaffylmGUI
                        Starting oneChannelGUI package
AptMidas                Graphical interface to APT midas
EG2probeset             This function allows to link GeneBank and
                        Entrez Gene ids to gene-level probe set ids
GOenrichment            Searching for Gene Ontology enriched terms
                        within a set of differentially expressed genes
IPAlistFilter           Filtering an expression set using a set of
                        Entrez genes extracted from Ingenuity Pathways
                        analysis (IPA)
ML.edesign              The function creates an data frame containing
                        the parameters useful for class prediction
OpenBeadStudioFiles     Read BeadStudio expression data file
OpenLargefiles          This function loads large data set made from
                        tab delimited files
PlotOptionsv1           A modified version of the function used in
                        affyPLM library
VennDiagram             Venn diagrams using two or three lists
biomartFilter           Filtering only gene-level probe sets with
                        multiple ensembl transcripts
buildingLocalAnnotation
                        Updates local gene-level annotation data for
                        gene and exon arrays using the netaffx database
colExtract              Extract a column from a tab delimited file with
                        header
combineGeoMSF           This function allows to combine GEO Matrix
                        Series Files belonging to the same experiment.
consistentFilters       This function allows filtering using the
                        combination of multiple paramenters, e.g. MiDAS
                        p-values and Rank Product p-values
cosieHscore             Parameters precalculated for the Affymetrix
                        core human annotation subgroup from FMI
                        Bioinformatics group and needed to correct SI
cosieHsfull             Parameters precalculated for the Affymetrix
                        full human annotation subgroup from FMI
                        Bioinformatics group and needed to correct SI
cosieMmcore             Parameters precalculated for the Affymetrix
                        core mouse annotation subgroup from FMI
                        Bioinformatics group and needed to correct SI
cosieMmfull             Parameters precalculated for the Affymetrix
                        full mouse annotation subgroup from FMI
                        Bioinformatics group and needed to correct SI
cosieWrapper            A wrapper to cosie, Corrected Splicing Indices
                        for Exon arrays, that for any given set of new
                        exon array experiments corrects for the
                        observed bias and improves the detection of
                        alternative splicing
createGeoTarget         Creating a affylmGUI Target starting from a GEO
                        Matrix series file
crosshybFilter          Removing from exon array gene/exon level probe
                        sets characterized by cross hybridization with
                        other transcripts
crosshybhuex.annotation
                        Annotation data for exon of human exon array
                        1.0 ST
crosshybmoex.annotation
                        Annotation data for exon of mouse exon array
                        1.0 ST
crosshybraex.annotation
                        Annotation data for exon of rat exon array 1.0
                        ST
dfMAplot                MA and Volcano plots from data present in a
                        limma derived topTable
erankProdAltSpl         Implementation of the Rank Product method for
                        the detection of alternative splicing events
erankProdAltSplFilter   Filtering Rank Product results for the
                        detection of alternative splicing events
exonContrasts           Defining t-test regularized p-values
exonTopTableExtract     Extracts data on the basis of a defined t-test
                        regularized p-value
exonsSpecific2as        Defining the exons associated to the various
                        alternative isoforms
extractAffyids          Extracting probe ids associated to a specific
                        Gene Ontology term
filteringTable          Filtering a tab delimited file
geneExonLibs            Download the Library files for gene and exon
                        analysis
genomePlot              This function plots average intensity signals
                        for two group experiment over the genes and
                        transcripts structure mapped on ENSEMBL to
                        identify a specific splicing event
geoVSbioc               linking GEO platforms to available BioC
                        annotations libraries
huex.annotation         Annotation data for CORE subset of human exon
                        array 1.0 ST
huex.variantexons       table linking exon-level probe set ids to
                        variant exons
inspecting.one.splice.index
                        Plotting on the profiles of splice indexes for
                        a transcript cluster ID
inspecting.splice.index
                        Plotting on a pdf file the profiles of splice
                        indexes
intensityFilter         intensity filtering with a mouse click
iqrFilter               Interquantile filtering with a mouse click
limmaExons              graphical interface to limma for alternative
                        splicing detection
listFilter              Subsetting an expression set using a list of
                        Affymetrix ids
makeBED15               This function creates files in BED15 format to
                        be loaded on the UCSC browser
mapping2RefSeq          This function maps on NCBI Reference sequences
                        spliced exons detected by the function
                        oneChannelGUI: Inspecting splice indexes
mapping2ensembl         Associating e-level probe sets to entrez gene
                        exonic structure
mapping2exon            This function maps on exon-level Probe
                        Selection Region (PSR) starting for the file
                        produced by function oneChannelGUI: Mapping
                        exon level probe sets to Reference Sequences
masigpro                The function executes maSigPro analysis
masigpro.edesign        The function creates an edesign object needed
                        to run maSigPro
masigpro.view           The function allows the visualization of
                        maSigPro results
metaArrayIC             Graphical interface to metaArray Integrative
                        Correlation function
metaArrayMerge          Tool to create a merge object for metaArray
                        package
moex.annotation         Annotation data for CORE subset of mouse exon
                        array 1.0 ST
moex.variantexons       table linking exon-level probe set ids to
                        variant exons
myExpresso              Running the affy expresso function with the
                        widget
normBoxplot             Box plot of the arrays data available in
                        NormalizeAffyData slot
ocPlotHist              Gene/Exon level density plots
ocPlotPCA               Gene/Exon level density plots
oneChannelGUI-package   Set of functions extending the capability of
                        affylmGUI package
plierToZero             Setting to 0 low log2 intensity values
                        generated with plier
plotGO                  Plotting parents of a GO term with few mouse
                        click
plotVariantSI           This function plots on UCSC genome browser data
                        derived by variantSI filter
raex.annotation         Annotation data for CORE subset of rat exon
                        array 1.0 ST
raex.variantexons       table linking exon-level probe set ids to
                        variant exons
rankProd                graphical interface to rank product method
                        implemented in RankProd Bioconductor library.
rankingConversion       This function transforms intensity data in
                        normalized ranks
rawBoxplotPN            Plotting raw log2 intensities from controls
rawpCheck               Raw p-value distribution from limma analysis by
                        a mouse click
refseqDownload          Retrieving Reference Sequences from NCBI ftp
retrievePSRseq          This function, given a file containing
                        exon-level probesets retrieves Probe selection
                        Regions, PRS, from RRE db
retrievePSRseq1gid      This function, given a gene-level probeset id,
                        retrieves Probe selection Regions, PRS, from
                        RRE db
reviqrFilter            Reverse interquantile filtering with a mouse
                        click
runningJetta            graphical interface to MADS/jetta R library.
sample.size.evaluation
                        The function executes and plots results from
                        ssize and delta fulction from the ssize packahe
sample.size.evaluation1
                        The function executes functions from the
                        sizepower packahe
showDataset             Grabbing info about the available expression
                        set
showTopTable            Modification of the function immplemented in
                        affylmGUI to generate a topTable
siggenes                The function executes SAM analysis implemented
                        in siggenes bioconductor library
simFilter               This function allows filtering on the basis of
                        the average splice index mean or min difference
                        between two groups
spliceIndex             This function coverts the exon intenisty data
                        in a slice index
standAloneAddingAnnotation
                        Attach to a data frame containing gene-level
                        data derived from Affymetrix exon arrays the
                        annotations derived by netaffx
standAloneBuildingLocalAnnotation
                        Creates a data frame with gene-level annotation
                        data for exon arrays using the netaffx database
targetWidget            Widget to create a target file to load .CEL
                        files
templA                  Generating a template A to be uploaded in
                        Ingenuity Pathways analysis (IPA)
trainTest               Creating a training set and a test set by a
                        mouse click
updateLibs              This function allows to update the present
                        installation of Bioconductor
variantExons            This function is used to generate a table
                        containing exon-level probe set data linked to
                        variant exons
variantSI               This function allows filtering on the basis of
                        variant exons
