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 numeric matrices of other spot-specific information. All matrices must have 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.

