exprSetRG-class          package:arrayMagic          R Documentation

_C_l_a_s_s _e_x_p_r_S_e_t_R_G _f_o_r _t_w_o _c_o_l_o_u_r _D_N_A _m_i_c_r_o_a_r_r_a_y _d_a_t_a
(_e_x_t_e_n_s_i_o_n _o_f _e_x_p_r_S_e_t)

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

     This is a class representation for two colour DNA microarray data.
     The class is based on the class 'exprSet' of the 'Biobase'
     package. The red and green channels  are stored in a single
     'exprSet' object. The information on the corresponding red-green
     pairs is stored separately. Several class methods offer a
     convienent way to access and set data.

_C_r_e_a_t_i_n_g _O_b_j_e_c_t_s:

     '  new('exprSetRG','
      '    channels = ..., # object of class matrix with columns
     "green" and "red" '
      '    exprs    = ..., # object of class matrix'
      '    se.exprs = ..., # object of class matrix'
      '    phenoData= ..., # object of class phenoData'
      '    notes    = ..., # object of class character'
      '    annotation    = ..., # object of class character'
      '  )'

_S_l_o_t_s:

     '_i_n_d_G_r_e_e_n': Object of class 'vector'; indexes of the green channel

     '_i_n_d_R_e_d': Object of class 'vector'; indexes of the red channel

     '_e_x_p_r_s': Object of class 'matrix'; the observed expression levels.
          This is a matrix with columns representing the red and green
          channels and rows representing genes. Each row in 'channels'
          lists the indexes of the corresponding pair of red and green
          channels representing a single microarray slide.

     '_s_e._e_x_p_r_s': Object of class 'matrix'; this is a matrix of the same
          dimensions as 'exprs', e.g. useful to represent the standard
          error estimates for the corresponding expression levels. 

     '_p_h_e_n_o_D_a_t_a': Object of class 'phenoData', i.e. an instance of
          class 'phenoData'  containing annotation information on the
          individual channels. The columns of the pData slot of this
          entity represent variables and the rows represent channels. 

     '_n_o_t_e_s': Object of class 'character' containing explanatory text;
          default: ""

     '_a_n_n_o_t_a_t_i_o_n': Object of class 'character'; default: ""

_E_x_t_e_n_d_s:

     Class 'exprSet', directly.

_M_e_t_h_o_d_s:


     _s_h_o_w (exprSetRG): renders information about the exprSetRG in a
          concise way on stdout, cf. class exprSet.

     _g_e_t_E_x_p_r_S_e_t_L_o_g_R_a_t_i_o (exprSetRG, seExprsHandling): Returns an
          'exprSet' object of the difference of the expression levels,
          i.e. the green channel minus the red channel.  The
          'phenoData' slot it the result of calling the class method
          'phenoDataSlide' on the object 'exprSetRG'. The 'se.exprs'
          slot contains the root-mean-square or the mean of the
          se.exprs of both channels depending on the argument
          'seExprsHandling'. The root-mean-square might be useful if
          the two se.exprs values are estimated standard deviations
          based on the same number observations and identical
          distribution. 'seExprsHandling' must be a character string;
          possible values are "rootMeanSquare" or "mean"; the default
          value is "rootMeanSquare". 

     _g_e_t_E_x_p_r_S_e_t_G_r_e_e_n_M_i_n_u_s_R_e_d same as method 'getExprSetLogRatio' 

     _g_e_t_E_x_p_r_S_e_t_R_e_d_M_i_n_u_s_G_r_e_e_n similar to method 'getExprSetLogRatio';
          the "negative" difference of the expression levels is
          returned, i.e. the red channel minus the green channel.


     _g_e_t_E_x_p_r_S_e_t_G_r_e_e_n (exprSetRG): Returns an 'exprSet' object which
          contains the expression levels of the green channel and the
          corresponding annotation.

     _g_e_t_E_x_p_r_S_e_t_R_e_d (exprSetRG): Returns an 'exprSet' object which
          contains the expression levels of the red channel and the
          corresponding annotation.

     _p_h_e_n_o_D_a_t_a_S_l_i_d_e (exprSetRG): Returns an 'phenoData' object
          characterizing all microarray slides. Those annotation
          information, which is the same for both channels (and not
          'NA') is taken directly, e.g. the the slide number. All other
          annotation variables are added specifically for each channel,
          i.e. prefixed with "greenSpecific_" and "redSpecific_". Do
          not use varLabels-names for subsetting.

     _p_D_a_t_a_S_l_i_d_e (exprSetRG): Returns an 'pData' object, i.e.
          'pData(phenoDataSlide(exprSetRG))'; cf. 'phenoDataSlide'. Do
          not use varLabels-names for subsetting.

     _p_h_e_n_o_D_a_t_a_G_r_e_e_n (exprSetRG): Returns an 'phenoData' object of the
          annotation information given for the green channel. Do not
          use varLabels-names for subsetting.

     _p_D_a_t_a_G_r_e_e_n (exprSetRG): Returns the 'pData' object taken out of
          the result of calling 'phenoDataGreen'. Do not use
          varLabels-names for subsetting.

     _p_h_e_n_o_D_a_t_a_R_e_d (exprSetRG): Returns an 'phenoData' object of the
          annotation information given for the red channel. Do not use
          varLabels-names for subsetting.

     _p_D_a_t_a_R_e_d (exprSetRG): Returns the 'pData' object taken out of the
          result of calling 'phenoDataRed'. Do not use varLabels-names
          for subsetting.

     _s_l_i_d_e_S_u_b_s_e_t (exprSetRG,i,j): Subsetting operation; where i
          corresponds to the rows  and j corresponds to the microarray
          slides. j is given by indexes or logicals related to the
          order of the channel pairs in 'channels'; cf. the constructor
          slot 'channels'.

     _g_e_t_I_n_d_G_r_e_e_n (exprSetRG): An accessor function for slot 'indGreen'.
          The corresponding elements of indGreen and indRed define
          microarray slides.

     _g_e_t_I_n_d_R_e_d (exprSetRG): An accessor function for slot 'indRed'. The
          corresponding elements of indGreen and indRed define
          microarray slides.

     [ (exprSetRG,i,j,type): A subset operator. Ensures that both the
          data and the annotation information ('phenoData') are
          subseted properly. This may only mix up the pairing of the
          channels, i.e. the validity of an exprSetRG, if you use
          argument option type == "invalidExprSetRG". Default:
          "validExprSetRG". See also: 'slideSubset'.

     _c_b_i_n_d (...): Concatenates 'exprSetRG' objects. Genes (rows) are
          assumed to match; cf. 'cbind.exprSetRG' 

     _a_s._e_x_p_r_S_e_t (exprSetRG): Class cast, returns an object of
          'exprSet', the information on the red and green channels is
          discarded.

     _a_s._R_G_L_i_s_t (exprSetRG, func): Returns an object of 'RGList' which
          in general refers to raw data. Hence, func(expression values)
          is returned, i.e. 'exp(x)' by default. All background values
          in the RGList object are set to zero.

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

     Andreas Buness <a.buness@dkfz.de>

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

     'exprSet-class', 'arrayData-class'

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

       indGreen=1:3
       indRed=4:6
       channels <- matrix( c(indGreen,indRed), nrow=length(indGreen), byrow=FALSE )
       colnames(channels) <- c("green","red")
       eSA <- new("exprSetRG", exprs=matrix(1:60, ncol=6, nrow=10), phenoData=
               new("phenoData", pData=data.frame(matrix(0,nrow=6,ncol=1)),
                   varLabels=list(rep("varLabel1",1))), channels=channels)
       stopifnot( all(pDataSlide(eSA) ==pData(eSA)[1:3,,drop=FALSE]) )
       eSAGreen <- getExprSetGreen(eSA)
       eSARed <- getExprSetRed(eSA)
       eSALogRatio <- getExprSetLogRatio(eSA)
       eSALogRatio2 <- getExprSetGreenMinusRed(eSA)
       eSALogRatio3 <- getExprSetRedMinusGreen(eSA)
       stopifnot( identical( eSALogRatio, eSALogRatio2 ) )
       stopifnot( identical( exprs(eSALogRatio), exprs(eSAGreen)-exprs(eSARed)) )
       stopifnot( all.equal.numeric( as.vector(exprs(eSALogRatio3)), as.vector(exprs(eSARed)-exprs(eSAGreen)) ))
       eSAPart <- eSA[,c(1,3,1,4,6,4)]
       eSAInvalid <- eSA[,c(1,3,1,5,6,4),type="invalidExprSetRG"]
       eSAPart2 <- slideSubset(eSA,j=c(1,3,1))

       eSAeSA <- cbind(eSA, eSA)
       eSAeSAPart2 <- cbind(eSA, eSAPart2)
       stopifnot( class(as.exprSet(eSA)) == "exprSet" )

       
      

