R Graphical Manual

Last data update: 2014.03.03

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R Release (3.2.3)
CranContrib
BioConductor
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Results 1 - 10 of 37 found.
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pairwise.filter (Package: simpleaffy) : Filter pairwise comparison statistics between two experimental groups

Given the results of a pairwise.comparison, filter the resulting gene list on expression level, PMA calls (if available), fold change and t-test statistic.

● Data Source: BioConductor
● Keywords: misc
● Alias: pairwise.filter
● 0 images

plot.pairwise.comparison (Package: simpleaffy) : Plots a PairComp object

Draws a scatter plot between means from a pairwise comparison. Colours according to PMA calls and identifies 'signficant' genes yielded by a filtering

● Data Source: BioConductor
● Keywords: misc
● Alias: plot,PairComp, plot,PairComp-method, plot.pairwise.comparison
● 0 images

plot.qc.stats (Package: simpleaffy) : Plots a QCStats object

Generates a visual summary of the various QC statistics recommended by Affymetrix in their 'Data Analysis Fundamentals' handbook.

● Data Source: BioConductor
● Keywords: misc
● Alias: plot,QCStats, plot,QCStats,missing-method, plot.qc.stats
● 1 images

qc (Package: simpleaffy) : Generate QC stats from an AffyBatch object

Generate QC metrix for Affymetrix data.

● Data Source: BioConductor
● Keywords: misc
● Alias: qc, qc,AffyBatch-method
● 1 images

qc.affy (Package: simpleaffy) : Generate Affymetrix Style QC Statistics

Generate QC data for Affymetrix arrays

● Data Source: BioConductor
● Keywords: misc
● Alias: qc.affy
● 1 images

qc.get.alpha1 (Package: simpleaffy) : Get or set the alpha values for the current QC environment

Alpha1 and Alpha2 are used to define the P/M/A thresholds for detection calling algorithm see - detection.p.val. These are array dependent, these functions set or get their values. Tau is a constant parameter within the calculation and is not array specific.

● Data Source: BioConductor
● Keywords: misc
● Alias: qc.get.alpha1, qc.get.alpha2, qc.get.tau, qc.set.alpha1, qc.set.alpha2
● 0 images

qc.get.array (Package: simpleaffy) : Get or set the name of the array for which the current QC

The array name is simply a free text name for the array of interest.

● Data Source: BioConductor
● Keywords: misc
● Alias: qc.get.array, qc.set.array
● 0 images

qc.get.probes (Package: simpleaffy) : Retrieve QC probeset names for the current array type

Get the names of probesets used to calculate 3'/5' ratios for the current array type. qc.get.spikes is used to set the spike probe names (i.e. bioB, bioC, etc.)

● Data Source: BioConductor
● Keywords: misc
● Alias: qc.add.probe, qc.get.probe, qc.get.probes
● 0 images

qc.get.ratios (Package: simpleaffy) : Retrieve pairs of probesets used for calculating 3'/5' ratios

Get the names of the qc probesets used to define the 3'/5' ratios.

● Data Source: BioConductor
● Keywords: misc
● Alias: qc.add.ratio, qc.get.ratio, qc.get.ratios
● 0 images

qc.get.spikes (Package: simpleaffy) : Retrieve QC spike probeset names for the current array type

Get the names of spike probesets for bioB, bioC, etc. ratios for the current array type. qc.get.probes is used to define the 3'/5' ratio probesets

● Data Source: BioConductor
● Keywords: misc
● Alias: qc.add.spike, qc.get.spike, qc.get.spikes
● 0 images