biasAdjust         package:diffGeneAnalysis         R Documentation

_b_a_i_s_A_d_j_u_s_t _p_e_r_f_o_r_m_s _b_i_a_s _a_d_j_u_s_t_m_e_n_t _o_f _n_o_r_m_a_l_i_z_e_d _d_a_t_a

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

     biasAdjust takes a normalized dataset and applies a multiplicative
     scalar derived from the data to help account for expression
     biases. These expression biases can come from many sources
     including dye bias,hybridization efficacy,changes in
     personnel,etc.After bias adjustment the data is ready for
     differential gene analysis.

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

     biasAdjust(normalized, numSlides)

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

normalized: normalized is a matrix of normalized microarray data.The
          first row consists of headers ans the first column consists
          of gene names.

numSlides: numSlides is the total number of chips of the microarray
          dataset.

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

     Returns a matrix of bias adjusted normalized data.

_N_o_t_e:

     biasAdjust takes 2-3 seconds to execute under optimal conditions
     of size of datasets and speed of the machine..Tested on a Pentium
     IV 1.6Ghz, 256Mb RAM with 22464 genes and 10 chips it took 12
     seconds to execute.

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

     Choudary L Jagarlamudi

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

     Dozmorov I,Centola,M. An associative analysis of gene expression
     array data. Bioinformatics.2003 Jan22;19(2):204-11

     Knowlton N,Dozmorov I, Centola M. Microarray data Analysis Tool
     box(MDAT): for normalization,adjustment and analysis of gene
     expression data. Bioonformatics.2004 Dec 12;20(18):3687-90

_E_x_a_m_p_l_e_s:

      
      #biasAdjust(normalized,7)

