GSint2BC             package:GeneSpring             R Documentation

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_D_e_s_c_r_i_p_t_i_o_n:

     These functions convert GeneSpring Experiment (Interpretation)
     objects into BioConductor expression objects and vice versa.

_U_s_a_g_e:

     expr.set <- GSint2BC(interpretation, what = "nor")
     gs.int <- BC2GSint(exprSet)

_A_r_g_u_m_e_n_t_s:

interpretation: GeneSpring Experiment 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 Experiment Interpretation object.

_D_e_t_a_i_l_s:

     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 converters 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 'ExpressionSet' object.
     Conversely, when a BioConductor object 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
     converters may provide better mapping.

_V_a_l_u_e:

     The return value depends on which function was called. The
     'BC2GSint()' function returns an object of class 'GSint'. The
     'GSint2BC()' function returns a BioConductor object of class
     'ExpressionSet'. See the documentation on 'GSint' and
     'ExpressionSet' for more information.

_N_o_t_e:

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

_A_u_t_h_o_r(_s):

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

_R_e_f_e_r_e_n_c_e_s:

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

_S_e_e _A_l_s_o:

     'GSload.exp', 'GSload.int', 'GSsave.exp'

_E_x_a_m_p_l_e_s:

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

     #Convert the objects into GeneSpring objects and back again
     gs.int <- BC2GSint(eset)
     expr.set <- GSint2BC(gs.int)

