GSint {GeneSpring}R Documentation

Creation of GSint class object

Description

The GSint class object contains the expression values and the annotations of the GeneSpring Expriment Interpretation object. Apart from the new function, the function GSint can be used to create a new GSint object.

Usage

GSint(expName = "GeneSpring experiment",
        a.nor = matrix(nc = 0, nr = 0),
        se.nor = matrix(nc = 0, nr = 0),
        sd.nor = matrix(nc = 0, nr = 0),
        n.nor = matrix(nc = 0, nr = 0),
        a.raw = matrix(nc = 0, nr = 0), 
        se.raw = matrix(nc = 0, nr = 0), 
        sd.raw = matrix(nc = 0, nr = 0), 
        n.raw = matrix(nc = 0, nr = 0),
        a.ctr = matrix(nc = 0, nr = 0),
        se.ctr = matrix(nc = 0, nr = 0),
        sd.ctr = matrix(nc = 0, nr = 0),
        n.ctr = matrix(nc = 0, nr = 0),
        expparam = data.frame(),
        numConditions = 0,
        ngenes = 0,
        genenames = c("")
)

Arguments

expName Experiment name
a.nor Matrix representing the AVERAGE expression values for the NORMALIZED expression values
se.nor Matrix representing the STANDARD ERROR for the NORMALIZED expression values
sd.nor Matrix representing the STANDARD DEVIATION for the NORMALIZED expression values
n.nor Matrix representing the NUMBER OF REPLICATES in this condition for the NORMALIZED values
a.raw Matrix representing the AVERAGE expression values for the RAW expression values
se.raw Matrix representing the STANDARD ERROR for the RAW expression values
sd.raw Matrix representing the STANDARD DEVIATION for the RAW expression values
n.raw Matrix representing the NUMBER OF REPLICATES in this condition for the RAW values
a.ctr Matrix representing the AVERAGE expression values for the CONTROL values
se.ctr Matrix representing the STANDARD ERROR for the CONTROL values
sd.ctr Matrix representing the STANDARD DEVIATION for the CONTROL values
n.ctr Matrix representing the NUMBER OF REPLICATES in this condition for the CONTROL values
expparam Data drame representin the sample attributes or experimental parameters
numConditions Numeric value representing the number of conditions (or samples) in this interpretaion or experiment
ngenes Numeric values representing the number of genes in the experiment
genenames List representing the gene names in the experiment

Details

The GSint class object is a representation of a GeneSpring Experiment Interpretation. The object consists of 17 slots:

1) The name of the experiment (slot: expName) 2) Twelve slots representing the various types of expression data as matrix objects 3) The experimental parameters (slot: expparam) 4) The number of samples or conditions in the experiment (slot: numConditions) 5) The number of genes (slot: ngenes) 5) A list of the gene names(slot: genenames)

All of the expression value slots are optional and are not guaranteed to contain data. When a GeneSpring Experiment is read in from file, only the a.nor slot and optionally the a.ctr slot will contain data. When a GeneSpring Experiment INTERPRETATION is read, any of the 12 expression values slots could contain data. Which data slots are filled is dependent on which choices were made in the construction of the external programs in GeneSpring.

For more information about GeneSpring external programs see the GeneSpring manual. For more information about the differences between an Experiment and an Interpretation see the R manual entries for GSload.int and GSload.exp.

Value

Both GSint and new return an object of class GSint.

Methods

show
signature(object = "GSint"): Produces a short description of the GSint class. It lists all the objects contained in the class.

Note

This and any other functions in the GeneSpring package are only useful, when using Agilent Technologies Gene Expression software GeneSpring.

Author(s)

Thon de Boer, Agilent Technologies, Santa Clara, CA, USA thon_deboer@agilent.com

References

For more information on using GeneSpring with R see http://www.chem.agilent.com/scripts/generic.asp?lpage=34733

See Also

GSload.int, GSload.exp, GSsave.exp, GSint2BC, BC2GSint

Examples

#Create some simple sample annotation
ep <- t(data.frame(SampleName=1:10))
#Create a GSint object with random data as the RAW data object
gs.int <- GSint(expName="Random data",a.raw=matrix(rnorm(1000),nc=10),expparam=ep, genenames=1:100)

gs.int@expName
t(gs.int@expparam)

[Package GeneSpring version 2.10.0 Index]