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
     'exprSet' 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)

