GSsave.exp {GeneSpring}R Documentation

Save a GeneSpring Interpretation to file

Description

The normalized values of the GeneSpring Interpretation object will be written to file. If the Interpretation object contains Control values, they will also be used. The experimental paramters and the experiment name will also be inlucded.

Usage

GSsave.exp(interpretation, filename = "GS_R_out.txt", EOF = "///", append = TRUE)

Arguments

interpretation The GeneSpring Experiment Interpretation object of class GSint
filename Name of the file. Can also be a connection object.
EOF String containing the delimiter used to separate the chunks in the file to be read.
append Boolean indicating if the experiment should be appended to the output, allowing for multiple objects to be send back to GeneSpring.

Details

A GeneSpring Experiment consists of the Normalized expression values for each sample and optionally the Control values for that normalized value. Each sample or hybridization has its own column (set) of expression values, wheras the expression values for an Experiment INTERPRETATION represent the mean value of the replicate values for that condition.

GeneSpring will be able to read multiple objects and it requires the R program to store all objects in one file, one object per "chunk", separated by a delimiter on its own line. The order in which the objects are defined (in the "Output" section of the External Program Interface definition), determines in which chunk the interpretation should be read by GeneSpring.

For more information see the manual entry for GSload.exp.

Value

This function does not return a usable value upon return.

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.exp, GSload.int

Examples


#Use the example data etc. from exprSet
library(Biobase)
data(geneData)
data(geneCov)
covdesc<- list("Covariate 1", "Covariate 2", "Covariate 3")
names(covdesc) <- names(geneCov)
pdata <- new("phenoData", pData=geneCov, varLabels=covdesc)
eset <- new("exprSet", exprs=geneData, phenoData=pdata)

#Convert the objects into GeneSpring objects
gs.int <- BC2GSint(eset)

#Save the Experiment in GeneSpring format
GSsave.exp(gs.int, filename = "GS_R_out.txt")


[Package GeneSpring version 2.12.0 Index]