probeSelectionInterface: Tcltk Interface to Generate an Instance of YaqcControlProbes...

In yaqcaffy: Affymetrix expression data quality control and reproducibility analysis

Description

probeSelectionInterface starts a tcltk graphical user interface (GUI) that allows the user to choose the probes to be used for subsequent quality analyses with the yaqcaffy package. The probes are selected on basis of the features of a given set of Affymetrix Genechips provided as input. The list of probes can be pre-filtered to display only control probes (i.e starting by AFFX) or all probes on the Genechip can be shown.

Usage

probeSelectionInterface(object,
returnVar="yaqcControlProbes",
filter=TRUE)

Arguments

object	an object of class AffyBatch or ExpressionSet.
returnVar	a string defining the name of the variable the returned object will be saved as in the global environment. The default variable name is 'yaqcControlProbes'. If such a variable name already exists, a warning will be issued and the user can cancel the function.
filter	logical value. If 'TRUE', the feature names of the input object are filtered out (see details). If 'FALSE', all features are listed for all control probes.

Details

Three tabs are displayed, one for the hybridization (bio) probes, labelling probes (dap, phe, thr and lys) and the degradation probes (actin and gapdh) respectively. If the user uses the 'Close' button, no return object is saved in the global environment. An object is saved as returnVar if the user presses 'Ok'. If such a variable name already exists, a warning will be issued and the user can close the interface and cancel the function.

If filtering is applied, the hybridization menus will list probes that match the given probe (BioB, BioC or BioD) and position (5, 3 or M). Similarly, only matching labelling probes (dap, phe, thr and lys) and positions will be displayed. As the pattern for the degradation probes are less strict, all the 'AFFX' probes, except those already selected as hybridization and labelling probes, will be displayed in the drop-down menus.

Value

Returns an object of class YaqcBioProbes.

Author(s)

Laurent Gatto

Examples

 ## Not run: 
   library(affydata)
   data(Dilution)
   probeSelectionInterface(Dilution)
 
## End(Not run)

yaqcaffy documentation built on Nov. 8, 2020, 8:31 p.m.