MAList-class              package:limma              R Documentation

_M-_v_a_l_u_e, _A-_v_a_l_u_e _E_x_p_r_e_s_s_i_o_n _L_i_s_t - _c_l_a_s_s

_D_e_s_c_r_i_p_t_i_o_n:

     A simple list-based class for storing M-values and A-values for a
     batch of spotted microarrays. 'MAList' objects are usually created
     during normalization by the functions 'normalizeWithinArrays' or
     'MA.RG'.

_S_l_o_t_s/_L_i_s_t _C_o_m_p_o_n_e_n_t_s:

     'MAList' objects can be created by 'new("MAList",MA)' where 'MA'
     is a list. This class contains no slots (other than '.Data'), but
     objects should contain the following components:

       'M':  numeric matrix containing the M-values (log-2 expression ratios).  Rows correspond to spots and columns to arrays.
       'A':  numeric matrix containing the A-values (average log-2 expression values).

     Optional components include:

       'weights':  numeric matrix of same dimensions as 'M' containing relative spot quality weights.  Elements should be non-negative.
       'other':    list containing other matrices, all of the same dimensions as 'M'.
       'genes':    data.frame containing probe information. Should have one row for each spot. May have any number of columns.
       'targets':  data.frame containing information on the target RNA samples.  Rows correspond to arrays.  May have any number of columns. Usually includes columns 'Cy3' and 'Cy5' specifying which RNA was hybridized to each array.
       'printer':  list containing information on the process used to print the spots on the arrays.  See PrintLayout.

     Valid 'MAList' objects may contain other optional components, but
     all probe or array information should be contained in the above
     components.

_M_e_t_h_o_d_s:

     This class inherits directly from class 'list' so any operation
     appropriate for lists will work on objects of this class. In
     addition, 'MAList' objects can be subsetted and combined. 'RGList'
     objects will return dimensions and hence functions such as 'dim',
     'nrow' and 'ncol' are defined.  'MALists' also inherit a 'show'
     method from the virtual class 'LargeDataObject', which means that
     'RGLists' will print in a compact way.

     Other functions in LIMMA which operate on 'MAList' objects include
     'normalizeWithinArrays', 'normalizeBetweenArrays',
     'normalizeForPrintorder', 'plotMA' and 'plotPrintTipLoess'.

_A_u_t_h_o_r(_s):

     Gordon Smyth

_S_e_e _A_l_s_o:

     02.Classes gives an overview of all the classes defined by this
     package.

     'marrayNorm-class' is the corresponding class in the marrayClasses
     package.