readCelHeader           package:affxparser           R Documentation

_P_a_r_s_i_n_g _t_h_e _h_e_a_d_e_r _o_f _a_n _A_f_f_y_m_e_t_r_i_x _C_E_L _f_i_l_e

_D_e_s_c_r_i_p_t_i_o_n:

     Reads in the header of an Affymetrix CEL file using the Fusion
     SDK.

_U_s_a_g_e:

     readCelHeader(filename)

_A_r_g_u_m_e_n_t_s:

filename: the name of the CEL file.

_D_e_t_a_i_l_s:

     This function returns the header of a CEL file. Affymetrix
     operates with different versions of this file format. Depending on
     what version is being read, different information is accessible.

_V_a_l_u_e:

     A named list with components described below. The entries are
     obtained from the Fusion SDK interface functions. We try to obtain
     all relevant information from the file. 

filename: the name of the cel file.

 version: the version of the cel file.

    cols: the number of columns on the chip.

    rows: the number of rows on the chip.

   total: the total number of features on the chip. Usually equal to
          'rows' times 'cols', but since it is a separate attribute in
          the SDK we decided to include it anyway.

algorithm: the algorithm used to create the CEL file.

parameters: the parameters used in the algorithm. Seems to be
          semi-colon separated.

chiptype: the type of the chip.

  header: the entire header of the CEL file. Only available for
          non-calvin format files.

cellmargin: a parameter used to generate the CEL file. According to
          Affymetrix, it designates the number of pixels to ignore
          around the feature border when calculating the intensity
          value (the number of pixels ignored are cellmargin divided by
          2).

noutliers: the number of features reported as outliers.

 nmasked: the number of features reported as masked.

_N_o_t_e:

     Memory usage:the Fusion SDK allocates memory for the entire CEL
     file, when the file is accessed. The memory footprint of this
     function will therefore seem to be (rather) large.

     Speed: CEL files of version 2 (standard text files) needs to be
     completely read in order to report the number of outliers and
     masked features.

_A_u_t_h_o_r(_s):

     James Bullard, bullard@stat.berkeley.edu and Kasper Daniel Hansen,
     khansen@stat.berkeley.edu

_S_e_e _A_l_s_o:

     'readCel()' for reading in the entire CEL file. That function also
     returns the header.  See 'affxparserInfo' for general comments on
     the package and the Fusion SDK.

_E_x_a_m_p_l_e_s:

       # Scan current directory for CEL files
       files <- list.files(pattern="[.](c|C)(e|E)(l|L)$")
       if (length(files) > 0) {
         header <- readCelHeader(files[1])
         print(header)
         rm(header)
       }

       # Clean up
       rm(files)

