norm1a                 package:nudge                 R Documentation

_F_u_n_c_t_i_o_n _f_o_r _n_o_r_m_a_l_i_z_i_n_g _t_h_e _m_e_a_n _o_f _s_i_n_g_l_e _r_e_p_l_i_c_a_t_e _l_o_g _r_a_t_i_o_s

_D_e_s_c_r_i_p_t_i_o_n:

     This is essentially the same as the lowess normalization suggested
     in the paper "Statistical methods for identifying differentially
     expressed genes in replicated cDNA microarrays" by Dudoit et al
     (2002), except the loess function is used instead of lowess and
     the recommended span is between 0.6 and 0.8. The normalization is
     done for each gene by subtracting from its log ratio the loess
     estimated mean for the log ratio based on the regression of log
     ratios on log intensities.

_U_s_a_g_e:

     norm1a(logratio, logintensity, span = 0.6)

_A_r_g_u_m_e_n_t_s:

logratio: A vector or single-column matrix of log (base 2) ratios of
          gene expressions in two samples.

logintensity: A vector or single-column matrix of log (base 2) total
          intensities (defined as the product) of gene expressions in
          the two samples.

    span: Proportion of data used to fit the loess regression of the
          log ratios on the log intensities.

_V_a_l_u_e:

     A vector or single-column matrix of mean normalized log ratios.

_A_u_t_h_o_r(_s):

     N. Dean and A. E. Raftery

_R_e_f_e_r_e_n_c_e_s:

     N. Dean and A. E. Raftery (2005). Normal uniform mixture
     differential gene expression detection for cDNA microarrays. BMC
     Bioinformatics. 6, 173-186.

     <URL: http://www.biomedcentral.com/1471-2105/6/173>

     S. Dudoit, Y. H. Yang, M. Callow and T. Speed (2002). Statistical
     methods for identifying differentially expressed genes in
     replicated cDNA microarray experiments. Stat. Sin. 12, 111-139.

_S_e_e _A_l_s_o:

     'norm1b','norm1c','norm1d','norm2c','norm2d'

_E_x_a_m_p_l_e_s:

     data(like)
     lR<-log(like[,1],2)-log(like[,2],2)
     lI<-log(like[,1],2)+log(like[,2],2)

     lRnorm<-norm1a(lR,lI)

