array2channel             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 _F_i_l_e _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 from with one row per array to one
     with one row per channel.

_U_s_a_g_e:

     array2channel(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 column names are founding 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:

     This function is used to convert the usual two-color
     representation of target information into a form suitable for
     single-channel analysis.

_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:

     'coerce,RGList,exprSet-method'

     An overview of methods for single channel analysis in limma is
     given by 6.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"))
     array2channel(targets)

