RGList-class              package:limma              R Documentation

_R_e_d, _G_r_e_e_n _I_n_t_e_n_s_i_t_y _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 red and green channel
     foreground and background intensities for a batch of spotted
     microarrays. 'RGList' objects are normally created by
     'read.maimages'.

_S_l_o_t_s/_L_i_s_t _C_o_m_p_o_n_e_n_t_s:

     'RGList' objects can be created by 'new("RGList",RG)' where 'RG'
     is a list. Objects of this class contains no slots (other than
     '.Data'), but objects should contain the following list
     components:

       'R':  numeric matrix containing the red (cy5) foreground intensities.  Rows correspond to spots and columns to arrays.
       'G':  numeric matrix containing the green (cy3) foreground intensities. Rows correspond to spots and columns to arrays.

     Optional components include

       'Rb':       numeric matrix containing the red (cy5) background intensities
       'Gb':       numeric matrix containing the green (cy3) background intensities
       'weights':  numeric matrix of same dimension as 'R' containing relative spot quality weights.  Elements should be non-negative.
       'other':    list containing other matrices, all of the same dimensions as 'R' and 'G'.
       '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 'RGList' 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, 'RGList' objects can be subsetted, combined and merged.
     'RGList' objects will return dimensions and hence functions such
     as 'dim', 'nrow' and 'ncol' are defined.  'RGLists' also inherit a
     'show' method from the virtual class 'LargeDataObject', which
     means that 'RGLists' will print in a compact way.

     'RGList' objects can be converted to 'exprSet2' objects by
     'as(RG,"exprSet2")'.

     Other functions in LIMMA which operate on 'RGList' objects include
     'normalizeBetweenArrays', 'normalizeForPrintorder',
     'normalizeWithinArrays'.

_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.

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