EList-class              package:limma              R Documentation

_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:

     Simple list-based classes for storing expression values (E-values)
     for a set of one-channel microarrays. 'EListRaw' holds expression
     values on the raw scale. 'EList' holds expression values on the
     log scale, usually after background correction and normalization.
     'EListRaw' objects are normally created by 'read.maimages'. In the
     future, 'EList' objects are likely to be created
     'normalizeBetweenArrays'.

_S_l_o_t_s/_L_i_s_t _C_o_m_p_o_n_e_n_t_s:

     'EList' objects can be created by 'new("EList",E)' where 'E' is a
     list. These classes contains no slots (other than '.Data'), but
     objects should contain a list component 'E' as follows:

       'E':  numeric matrix containing the E-values (raw or log-2 expression ratios).  Rows correspond to spots and columns to arrays.

     Optional components include:

       'weights':  numeric matrix of same dimensions as 'E' containing relative spot quality weights.  Elements should be non-negative.
       'other':    list containing other matrices, all of the same dimensions as 'E'.
       'genes':    data.frame containing probe information. Should have one row for each probe. 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.

     Valid 'EList' or 'EListRaw' 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:

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

_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.

     'ExpressionSet-class' is a more formal class in the Biobase
     package.