LumiBatch-class             package:lumi             R Documentation

_C_l_a_s_s _L_u_m_i_B_a_t_c_h: _c_o_n_t_a_i_n _a_n_d _d_e_s_c_r_i_b_e _I_l_l_u_m_i_n_a _m_i_c_r_o_a_r_r_a_y _d_a_t_a

_D_e_s_c_r_i_p_t_i_o_n:

     This is a class representation for Illumina microarray data. It
     extends 'ExpressionSet'.

_E_x_t_e_n_d_s:

     Directly extends class 'ExpressionSet'.

_C_r_e_a_t_i_n_g _O_b_j_e_c_t_s:

     'new('LumiBatch', exprs = [matrix], se.exprs = [matrix], beadNum =
     [matrix], detection = [matrix], phenoData = [AnnotatedDataFrame],
     history = [data.frame], ...) '

     'LumiBatch' instances are usually created through
     'new("LumiBatch", ...)'. The arguments to 'new' should include
     'exprs' and 'se.exprs', others can be  missing, in which case they
     are assigned default values.

     Objects can be created using the function 'lumiR'.

_S_l_o_t_s:

     Slot specific to 'LumiBatch':

     '_h_i_s_t_o_r_y': a data.frame recording the operation history of the
          LumiBatch object.

     '_c_o_n_t_r_o_l_D_a_t_a': a data.frame with first two columns as
          "controlType" and "ProbeID". The rest columns are the control
          probe expression amplitudes for individual samples.

     '_Q_C': a the quality control information of the LumiBatch object,
          returned by lumiQ function.

     Slots inherited from 'ExpressionSet':

     '_a_s_s_a_y_D_a_t_a' contains equal dimensional matrices: '\bf exprs'
          (contains gene expression level, which is the mean of its
          bead replicates.), '\bf se.exprs' (contains gene expression
          standard error, which is the standard error of its bead
          replicates.),  '\bf beadNum' (records the number of beads for
          the probe.), '\bf detection' (records the detection p-value
          of the probe. The number is from [0,1]. By default, < 0.01
          indicates good detection.).  For more details of 'assayData',
          please see 'ExpressionSet'  

     '_p_h_e_n_o_D_a_t_a': See 'eSet'

     '_e_x_p_e_r_i_m_e_n_t_D_a_t_a': See 'eSet'

     '_a_n_n_o_t_a_t_i_o_n': See 'eSet'

_M_e_t_h_o_d_s:

     *Class-specific methods:*

     '_s_e._e_x_p_r_s(_L_u_m_i_B_a_t_c_h)', '_s_e._e_x_p_r_s(_L_u_m_i_B_a_t_c_h,_m_a_t_r_i_x)<-': Access and
          set elements named 'se.exprs' in the 'AssayData-class' slot.

     '_b_e_a_d_N_u_m(_L_u_m_i_B_a_t_c_h)', '_b_e_a_d_N_u_m(_L_u_m_i_B_a_t_c_h)<-': Access and set
          elements named 'beadNum' in the 'AssayData-class' slot. Use
          "beadNum(LumiBatch) <- NULL" to remove the beadNum element.

     '_d_e_t_e_c_t_i_o_n(_L_u_m_i_B_a_t_c_h)', '_d_e_t_e_c_t_i_o_n(_L_u_m_i_B_a_t_c_h)<-': Access and set
          elements named 'detection' in the 'AssayData-class' slot. Use
          "detection(LumiBatch) <- NULL" to remove the detection
          element.

     '_g_e_t_H_i_s_t_o_r_y(_L_u_m_i_B_a_t_c_h)': Access the operation history of
          'LumiBatch' object.

     *Derived from 'ExpressionSet'* (For the directly inherited
     methods,  please see 'ExpressionSet' and 'eSet'):

     '_c_o_m_b_i_n_e(_L_u_m_i_B_a_t_c_h,_m_i_s_s_i_n_g)': Combine two LumiBatch objects,
          including 'history' slot. See 'eSet'

     '_e_x_p_r_s(_L_u_m_i_B_a_t_c_h)', '_e_x_p_r_s(_L_u_m_i_B_a_t_c_h,_m_a_t_r_i_x)<-': Access and set
          elements named 'exprs' in the 'AssayData-class' slot.

     '_o_b_j_e_c_t[(_i,_j)': Conduct subsetting of the data in a LumiBatch
          object 

     *Standard generic methods* (For the directly inherited methods, 
     please see 'ExpressionSet' and 'eSet'):

     '_i_n_i_t_i_a_l_i_z_e(_L_u_m_i_B_a_t_c_h)': Object instantiation, used by 'new'; not
          to be called directly by the user.

     '_v_a_l_i_d_O_b_j_e_c_t(_L_u_m_i_B_a_t_c_h)': Validity-checking method, ensuring that
          'exprs' and 'se.exprs'  is a member of 'assayData'. Other
          validity check is the same as 'checkValidity(ExpressionSet)'.

     '_s_h_o_w(_L_u_m_i_B_a_t_c_h)' A summary of the 'LumiBatch' object.

_A_u_t_h_o_r(_s):

     Pan Du, Simon Lin

_S_e_e _A_l_s_o:

     'lumiR', 'lumiT', 'lumiN', 'boxplot-methods', 'pairs-methods',
     'MAplot-methods'

_E_x_a_m_p_l_e_s:

     ## load example data
     data(example.lumi)

     ## show the summary of the data
     # summary(example.lumi)
     example.lumi    

     ## get express matrix
     temp <- exprs(example.lumi)

     ## get a subset
     temp <- example.lumi[,1]        ## retrieve the first sample

     ## get the probe id
     featureNames(example.lumi)[1:3]

     ## combine LumiBatch objects
     temp <- combine(example.lumi[,1], example.lumi[,3])
     temp

