affxparserInfo          package:affxparser          R Documentation

_O_v_e_r_v_i_e_w _o_f _t_h_e _A_f_f_x_p_a_r_s_e_r _p_a_c_k_a_g_e.

_D_e_s_c_r_i_p_t_i_o_n:

     The package implements an interface to the Fusion SDK from
     Affymetrix.com.

_U_s_a_g_e:

       affxparserInfo(fusion.license = FALSE, file.changes = FALSE)

_A_r_g_u_m_e_n_t_s:

fusion.license: display the license of the Fusion SDK (this will happen
          in a browser).

file.changes: display the changes made to the Fusion SDK.

_D_e_t_a_i_l_s:

     This package implements an interface to the Fusion SDK from
     Affymetrix.com. This SDK (software development kit) is an open
     source library used for parsing the various files formats used by
     the Affymetrix platform.

     The intention is to provide interfaces to most if not all file
     formats which may be parsed using Fusion.

     The SDK supports parsing of all the different versions of a
     specific fileformat. This means that ascii, binary as well as the
     new binary format (codename Calvin) used by Affymetrix is
     supported through a single API. We also expect any future changes
     to the file formats to be reflected in the SDK, and subsequently
     in this package.

     However, as the current Fusion SDK does not support compressed
     files, neither does 'affxparser'. This is in contrast to some of
     the existing code in 'affy' and relatives (see below for links).

     In general we aim to provide functions returning all information
     in the respective files. Currently it seems that future Affymetrix
     chip designs may consists of so many features that returning all
     information will lead to an unnecessary overhead on the case a
     user only wants access to a subset. We have tried to make this
     possible.

     For older file, certain entries in the files have been removed
     from newer specifications, and the SDK does not provide utilities
     for reading these entries. This includes eg. the FEAT column of
     CDF files.

     Currently the package as well as the Fusion SDK is in beta stage.
     Bugs may be related to either codebase. We are very interested in
     users being unable to compile/parse files using this library -
     this includes users with custom chip designs.

     In addition, since we aim to return all information stored in the
     file (and accessible using the Fusion SDK) we would like reports
     from users being unable to do that.

     The efficiency of the underlying code may vary with the version of
     the file being parsed. For example, we currently report the number
     of outliers present in a CEL file. In order to obtain this
     information from text based CEL files (version 2), the entire file
     needs to be read into memory. With version 3 of the file format,
     this information is stored in the header.

     With the introduction of the Fusion SDK (and the next version of
     their file formats) Affymetrix has made it possible to use
     multibyte character sets. This implies that character information
     may be inaccesible if the compiler used to compile the c++ code
     does not support multibyte character sets (specifically we require
     that the R installation has defined the macro 'SUPPORT_MCBS' in
     the 'Rconfig.h' header file).

     The 'affxparserInfo' function returns relevant information
     regarding the version of the Fusion SDK (and possibly more). It
     simply echoes the README file in the package directory.

_A_u_t_h_o_r(_s):

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

_R_e_f_e_r_e_n_c_e_s:

     <URL: http://www.affymetrix.com>, particular the support and
     developer parts of the website.

_S_e_e _A_l_s_o:

     Existing functions for parsing Affymetrix files may be found in
     'affy', 'oligo', 'makecdfenv' and 'makePlatformDesign'.

_E_x_a_m_p_l_e_s:

       affxparserInfo()

