GSint2BC {GeneSpring} | R Documentation |
These functions convert GeneSpring Experiment (Interpretation) objects into BioConductor expression objects and vice versa.
expr.set <- GSint2BC(interpretation, what = "nor") gs.int <- BC2GSint(exprSet)
interpretation |
GeneSpring Expereiment Interpretation object |
what |
For GSload.intBC() only. Indicates what data from the
GeneSpring Experiment Interpretation should be used.
Valid values for what can be nor and raw , representing
Normalized or Raw expression values. The Control values cannot be used. |
exprSet |
GeneSpring Expereiment Interpretation object |
The GeneSpring Experiment Interpretation and the BioConductor objects are quite similar, but there are some differences. GeneSpring interpretations can contain information on both normalized and original raw values, and can include, Standard Error, Standard Deviation and number of replicates information, but the BioConductor objects can contain more sample attribute information in the form of the MIAME annotations.
These functions provide convertors for both types of objects.
When converting a GeneSpring object into a BioConductor object, the user has the choice of either using the normalized or raw expression values for the BioConductor exprSet object. Conversely, when a BioConductor objects is converted into a GeneSpring object, the expression values are loaded as normalized values.
The phenoData objects describing the phenotypical data for the samples in a BioConductor object are converted into Experimental Parameter objects in the GeneSpring class object, and vice versa.
The experiment name and any of the other annotations for the BioConductor objects that are stored in the MIAME objects are currently not converted, although future versions of these convertors may provide better mapping.
The return value depends on which fucntion was called.
The BC2GSint()
function returns an object of class GSint
.
The GSint2BC()
function returns a BioConductor object of class exprSet
.
See the documentation on GSint
and exprSet
for more information.
This and any other functions in the GeneSpring package are only useful, when using Silicon Genetics Gene Expression software GeneSpring.
Thon de Boer, Silicon Genetics, Redwood city, CA, USA thon@silicongenetics.com
For more information on using GeneSpring with R see http://www.silicongenetics.com/cgi/SiG.cgi/Support/GeneSpring/GSnotes/R.smf
GSload.exp
,
GSload.int
,
GSsave.exp
#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 and back again gs.int <- BC2GSint(eset) expr.set <- GSint2BC(gs.int)