HarshExt             package:Harshlight             R Documentation

_a _b_l_e_m_i_s_h _d_e_t_e_c_t_i_o_n _p_r_o_g_r_a_m _f_o_r _m_i_c_r_o_a_r_r_a_y _c_h_i_p_s: _e_x_t_e_n_d_e_d _d_e_f_e_c_t_s _o_n_l_y

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

     Harshlight automatically detects and masks blemishes in microarray
     chips of class 'AffyBatch'

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

     HarshExt(affy.object, my.ErrorImage = NULL, extended.radius = 10)

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

affy.object: An AffyBatch object containing two or more chips.

my.ErrorImage: A batch of ErrorImages obtained through other programs.
          The error images must be in a matrix format, in which the
          first index represents each cell in the matrix and the second
          index represents the chip number. By default, the program
          calculates the error images for the batch of chips
          affy.object as described in Suarez-Farinas M et al., BMC
          Bioinformatics - 2005. If a batch of error images is
          provided, the affy.object is also required.

extended.radius: Radius of the median kernel used to identify extended
          defects on the chip.

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

     HarshExt is used to detect only extended defects on the surface of
     the chip. It does not detect compact or diffuse defects (see the
     help page for Harshlight).

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

     Mayte Suarez-Farinas, Maurizio Pellegrino, Knut M. Wittkwosky,
     Marcelo O. Magnasco mpellegri@rockefeller.edu

_R_e_f_e_r_e_n_c_e_s:

     <URL: http://asterion.rockefeller.edu/Harshlight/>

     Harshlight: a "corrective make-up" program for microarray chips,
     Mayte Suarez-Farinas, Maurizio Pellegrino, Knut M Wittkowski and
     Marcelo O Magnasco, BMC Bioinformatics 2005 Dec 10; 6(1):294

     "Harshlighting" small blemishes on microarrays, Suarez-Farinas M,
     Haider A, Wittkowski KM., BMC Bioinformatics. 2005 Mar 22;6(1):65.

