marrayTools           package:marrayTools           R Documentation

_W_r_a_p_p_e_r _f_u_n_c_t_i_o_n

_D_e_s_c_r_i_p_t_i_o_n:

     This functions will produce a directory of diagnostic plots,
     quality measures and normalization.

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

     spotTools(fnames, path = ".", galfile, bg = TRUE, plot = TRUE, quality = TRUE, fill = TRUE, raw = FALSE, echo = TRUE, ...)

     gpTools(fnames, path = ".", galfile, bg = TRUE, plot = TRUE, quality = TRUE, fill = TRUE, raw = FALSE, echo = TRUE, ...)

_A_r_g_u_m_e_n_t_s:

  fnames: a vector of character strings containing the file names of
          each spot quantification data file.  These typically end in
          '.spot' for the software 'Spot' or '.gpr' for the software
          'GenePix'.

    path: a character string representing the data directory. By
          default this is set to the current working directory ("."). 
          In the case where 'fnames' contains the full path name, path
          should be set to NULL.

 galfile: a character string representing the Gal file.

      bg: logical: if 'TRUE', background correction is performed before
          normalization

    plot: logical: if 'TRUE', maDiagnPlots is call to generate basic
          diagnostic plot per array.

 quality: logical: if 'TRUE', maQuality is call to calculate basic
          quality measures.

    fill: logical: if `TRUE', `scan' will implicitly add empty fields
          to any lines with fewer fields than implied by `what'.

     raw: logical: if 'TRUE', the microarray object class of
          'marrayRaw' is return rather than 'marrayNorm'.

    echo: logical: if 'TRUE' (default), run-time information of the
          array currently being process is printed.

     ...: further arguments to 'scan' or 'maNorm'.

_V_a_l_u_e:

     Jpeg files of diagnostic plots, excel files of quality measures,
     tab delimited files of normalized log-ratios and log-intensities
     values are saved to disk. In addition, an object of class
     'marrayRaw' or 'marrayNorm' is return.

_A_u_t_h_o_r(_s):

     Yee Hwa (Jean) Yang

_S_e_e _A_l_s_o:

     'read.marrayRaw'

_E_x_a_m_p_l_e_s:

      data(swirl)
      datadir <- system.file("data", package="marrayInput")

     ## normdata <- spotTools(path=datadir, quality=FALSE)

