spotMerge             package:arrayMagic             R Documentation

_A_v_e_r_a_g_i_n_g _o_f _s_p_o_t _r_e_p_l_i_c_a_s

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

     The mean of replicated spots with identical number of replicas is
     calculated for each channel separately (note: 'spotMerge' does
     require an equal number of replicas). All other spots need to be
     eliminated with the help of the argument 'spotsToBeRemoved'. The
     mean is calculated for the expression levels 'exprs' of the
     'exprSetRGObject' and for the 'intensities' and 'weights' of the
     'arrayDataObject'. Any existing 'se.exprs'-'matrix' as part of
     'exprSetRGObject' is discarded. The standard deviation of the spot
     merge operation for the expression values is returned as
     'se.exprs'. The corresponding rows of 'spotAttr' in
     'arrayDataObject' are concatenated and form a single row of
     respectively more columns.

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

     spotMerge(exprSetRGObject, arrayDataObject, spotIdentifier="Name", spotsToBeRemoved=c("Blank"))

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

arrayDataObject: object of type 'arrayData'; required; default: missing

exprSetRGObject: object of type 'exprSetRG'; required; default: missing

spotIdentifier: character string; required; default: "Name" 

spotsToBeRemoved: vector of character strings, all spots which match
          the strings are removed from  the analysis before merging;
          required; default: 'c("Blank")'

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

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

     A list containing the "merged" 'exprSetRGObject' and
     'arrayDataObject'.

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

     Andreas Buness <a.buness@dkfz.de>

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

     'processArrayData', 'slideMerge', 'exprSetRG-class',
     'arrayData-class'

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

         intensities <- array(data=runif(600),dim=c(100,2,3))
         dimnames(intensities) <- list(NULL, c("green","red"), NULL)
         spotAttr <- data.frame(Name=I(rep(c("x","y","k","l","z"),20)),
                                Zahl=rep(c(1,2,3,4,5),20),
                                Index=c(1:100))
         arrayDataObject <- new("arrayData", intensities=intensities, weights=intensities[,1,],
                                spotAttr=spotAttr, hybAttrList=NULL)
         indGreen=1:3
         indRed=4:6
         channels <- matrix( c(indGreen,indRed), nrow=length(indGreen), byrow=FALSE )
         colnames(channels) <- c("green","red")
         exprMatrix <- matrix(data=1,nrow=100,ncol=6,byrow=FALSE)
         pD <- data.frame(matrix(0,nrow=6,ncol=1))
         exprSetRGObject <- new("exprSetRG", exprs=exprMatrix, se.expr=exprMatrix,
                                   phenoData=new("phenoData",
                                     pData= pD,varLabels=list(rep("varLabel1",1))),
                                   channels=channels)
         resultList <- spotMerge(arrayDataObject=arrayDataObject,exprSetRGObject=exprSetRGObject, spotsToBeRemoved=c("x","z"))
         resultExprSetRG <- resultList[["exprSetRGObject"]]
         stopifnot( dim(exprs(resultExprSetRG))[1] == 3 )
         stopifnot( dim(exprs(resultExprSetRG))[2] == 6 )
         stopifnot(all(exprs(resultExprSetRG) == 1))
         stopifnot((all(se.exprs(resultExprSetRG) == 0)))
         resultArrayData <- resultList[["arrayDataObject"]]
         stopifnot( all(getIntensities(resultArrayData)[,1,] == getWeights(resultArrayData)) )
         nameColumns <- grep("Name", colnames(getSpotAttr(resultArrayData)))
         zahlColumns <- grep("Zahl", colnames(getSpotAttr(resultArrayData)))
         stopifnot( getSpotAttr(resultArrayData)[1,nameColumns] == rep ("y", 20 ) )
         stopifnot( getSpotAttr(resultArrayData)[1,zahlColumns] == rep (2, 20 ) )


         

             

