readHeader               package:limma               R Documentation

_R_e_a_d _H_e_a_d_e_r _I_n_f_o_r_m_a_t_i_o_n _f_r_o_m _I_m_a_g_e _A_n_a_l_y_s_i_s _R_a_w _D_a_t_a _F_i_l_e

_D_e_s_c_r_i_p_t_i_o_n:

     Read the header information from a GenePix Results (GPR) file or
     from an SMD raw data file. These functions are used internally by
     'read.maimages' and are not usually called directly by users.

_U_s_a_g_e:

     readGenericHeader(file, columns, sep="\t")
     readGPRHeader(file)
     readSMDHeader(file)

_A_r_g_u_m_e_n_t_s:

    file: character string giving file name. If it does not contain an
          absolute path, the file name is relative to the current
          working directory.

 columns: character vector specifying data column headings expected to
          be in file

     sep: the character string separating column names

_D_e_t_a_i_l_s:

     Raw data files exported by image analysis programs include a
     number of header lines which contain information about the
     scanning process. This function extracts that information and
     locates the line where the intensity data begins. 'readGPRHeader'
     is for GenePix output and 'readSMDHeader' is for files from the
     Stanford Microarray Database (SMD). 'readGenericHeader' finds the
     line in the file on which the data begins by searching for
     specified column headings.

_V_a_l_u_e:

     A list with components corresponds to lines of header information.
     A key component is 'NHeaderRecords' which gives the number of
     lines in the file before the intensity data begins. All other
     components are character vectors.

_A_u_t_h_o_r(_s):

     Gordon Smyth

_R_e_f_e_r_e_n_c_e_s:

     See <URL: http://www.axon.com/gn_GenePix_File_Formats.html> for
     GenePix formats.

     See <URL: http://www.bluegnome.co.uk> for information on BlueFuse.

     See <URL: http://genome-www.stanford.edu/Microarray> for the SMD.

_S_e_e _A_l_s_o:

     'read.maimages'

     An overview of LIMMA functions to read data is given in
     03.ReadingData.