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.

