slideMerge            package:arrayMagic            R Documentation

_A_v_e_r_a_g_i_n_g _o_f _t_w_o _c_o_l_o_u_r _m_i_c_r_o_a_r_r_a_y _r_e_p_l_i_c_a_s

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

     The mean of the expression values is calculated separately for
     each channel. If no 'se.exprs' values are given in
     'exprSetRGObject', 'se.exprs' is set to the standard deviation of
     the expression values (which is possibly 'NA'). If available it is
     set to the root-mean-square or the mean of the given 'se.exprs'
     values depending on the argument 'seExprsHandling'. The
     root-mean-square can be useful if the  'se.exprs' values are
     estimated standard deviations based on the same number of
     observations taken from identical distributions.

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

     slideMerge(exprSetRGObject, slideMergeColumn, sampleAnnotationColumns, seExprsHandling="rootMeanSquare", verbose=TRUE)

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

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

slideMergeColumn: character string specifying the variable of the
          'phenoData' object of the 'exprSetRGObject', which is used to
          determine replicas; required; default missing

sampleAnnotationColumns: vector of character strings; optional; default
          missing. A vector which contains all 'phenoData' variables
          relevant for further analysis. The 'phenoData'-annotation
          should be consistent for slide replicas. By default the
          argument 'sampleAnnotationColumns' is missing and all
          'phenoData' variables are used.

seExprsHandling: character string; either "rootMeanSquare" or "mean";
          required; default "rootMeanSquare" 

 verbose: logical; required; default: 'TRUE' 

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

     The 'phenoData'-annotation should be consistent for slide
     replicas, The annotation within the group of replicas is checked
     for consistency to assure a meaningful slide merge operation. Any
     ambiguities are reported. This reporting shall help to avoid and
     discover slide annotation errors. For example if samples are
     hybridized twice, the "slideNumber" will not be consistent within
     the "sampleID" which is used to determine replicas via the
     argument 'slideMergeColumn'.

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

     object of class 'exprSetRG-class', i.e. the "merged"
     'exprSetRGObject'

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

     Andreas Buness <a.buness@dkfz.de>

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

     'spotMerge', 'exprSetRG-class'

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

       indGreen=1:2
       indRed=3:4
       channels <- matrix( c(indGreen,indRed), nrow=length(indGreen), byrow=FALSE )
       colnames(channels) <- c("green","red")
       exprsMatrix <- matrix(rep(1:10,4),nrow=10,ncol=4,byrow=FALSE)
       phenoMatrix <- matrix(c(c(1,2),c(3,3),c(5,5)),nrow=2,ncol=3,byrow=FALSE)
       colnames(phenoMatrix) <- c("one","two","usedForMerge")
       phenoMatrix <- rbind(phenoMatrix,phenoMatrix)
       eSA <- new("exprSetRG", exprs=exprsMatrix, phenoData=
                  new("phenoData", pData=data.frame(phenoMatrix, check.names=FALSE),
                      varLabels=as.list(colnames(phenoMatrix))),
                  channels=channels)
       eSM <- slideMerge(exprSetRGObject=eSA, slideMergeColumn="usedForMerge")
       eSAOne <- slideSubset(eSA,j=c(1))
       stopifnot( all(exprs(eSAOne) == exprs(eSM) ))
       stopifnot( all( se.exprs(eSM) == 0 ) )

      

             

