targetsA2C               package:limma               R Documentation

_C_o_n_v_e_r_t _T_w_o-_C_o_l_o_r _T_a_r_g_e_t_s _D_a_t_a_f_r_a_m_e _f_r_o_m _O_n_e-_R_o_w-_P_e_r-_A_r_r_a_y _t_o _O_n_e-_R_o_w-_P_e_r-_C_h_a_n_n_e_l

_D_e_s_c_r_i_p_t_i_o_n:

     Convert a two-color targets dataframe with one row per array to
     one with one row per channel.

_U_s_a_g_e:

     targetsA2C(targets, channel.codes=c(1,2), channel.columns=list(Target=c("Cy3","Cy5")), grep=FALSE)

_A_r_g_u_m_e_n_t_s:

 targets: data.frame with one row per array giving information about
          target samples associated covariates.

channel.codes: numeric or character vector of length 2 giving codes for
          the channels

channel.columns: named list of character vectors of length 2. Each
          entry gives a pair of names of columns in 'targets' which
          contain channel-specific information. This pair of columns
          should be assembled into one column in the output.

    grep: logical, if 'TRUE' then the channel column names are found by
          'grep'ing, i.e., the actual column names need only contain
          the names given by 'channel.columns' as substrings

_D_e_t_a_i_l_s:

     The 'targets' dataframe holds information about the RNA samples
     used as targets in the microarray experiment. It is often read
     from a file using 'readTargets'. This function is used to convert
     the dataframe from an array-orientated format with one row for
     each array and two columns for the two channels into a
     channel-orientated format with one row for each individual channel
     observations. In statistical terms, the first format treats the
     arrays as cases and treats the channels as repeated measurements.
     The second format treats the individual channel observations as
     cases. The second format may be more appropriate if the data is to
     be analyzed in terms of individual log-intensities.

_V_a_l_u_e:

     data.frame with twice as many rows as 'targets'. Any pair of
     columns named by 'channel.columns' will now be one column.

_A_u_t_h_o_r(_s):

     Gordon Smyth

_S_e_e _A_l_s_o:

     'targetsA2C' is used by the 'coerce' method from 'RGList' for
     'ExpressionSet' in the convert package.

     An overview of methods for single channel analysis in limma is
     given by 07.SingleChannel.

_E_x_a_m_p_l_e_s:

     targets <- data.frame(FileName=c("file1.gpr","file2.gpr"),Cy3=c("WT","KO"),Cy5=c("KO","WT"))
     targetsA2C(targets)