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

