samControl             package:siggenes             R Documentation

_S_A_M _a_n_d _E_B_A_M _A_r_g_u_m_e_n_t_s

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

     Specifies most of the optional arguments of 'sam' and 'ebam'.

     Currently, only used in 'limma2sam' and 'limma2ebam'.

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

     samControl(delta = NULL, n.delta = 10, p0 = NA, lambda = seq(0, 0.95, 0.05), 
        ncs.value = "max", ncs.weights = NULL, q.version = 1)
        
     ebamControl(p0 = NA, p0.estimation = c("splines", "interval", "adhoc"), 
        lambda = NULL, ncs.value = "max", use.weights = FALSE)

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

   delta: a numeric vector specifying a set of values for the threshold
           Delta that should be used in 'sam'. If 'NULL', 'n.delta'
          Delta values will be computed automatically. Please note that
          the meaning of the argument 'delta' differs between 'sam' and
          'ebam'.

 n.delta: a numeric value specifying the number of Delta values that
          will be computed over the range of all possible values for
          Delta in 'sam', if 'delta' is not specified.

      p0: a numeric value specifying the prior probability pi0  that a
          gene is not differentially expressed. If 'NA', 'p0' will be
          computed by the function 'pi0.est'.

p0.estimation: either '"splines"' (default), '"interval"', or
          '"adhoc"'.  If '"splines"', the spline based method of Storey
          and Tibshirani (2003) is used to estimate p0. If '"adhoc"'
          ('"interval"'), the adhoc (interval based) method  proposed
          by Efron et al. (2001) is used to estimate p0. In the case of
          'samControl', 'p0.estimation = "splines"' is always used. For
          details on this estimation, see 'pi0.est'.

  lambda: a numeric vector or value specifying the lambda values used
          in the estimation of the prior probability. For details, see
          'pi0.est'.

ncs.value: a character string. Only used if 'lambda' is a vector.
          Either '"max"' or '"paper"'. For details, see 'pi0.est'.

ncs.weights: a numeric vector of the same length as 'lambda' containing
          the weights used in the estimation of pi0. By default no
          weights are used. For details, see 'pi0.est'. Only considered
          in 'samControl'.

use.weights: should weights be used in the spline based estimation of
          p0? If 'TRUE', 1 - 'lambda' is used as weights. For details,
          see 'pi0.est'. Only considered in 'ebamControl'.

q.version: a numeric value indicating which version of the q-value
          should be computed. If 'q.version = 2', the original version
          of the q-value, i.e. min{pFDR}, will be computed. If
          'q.version = 1', min{FDR} will be used in the calculation of
          the q-value. Otherwise, the q-value is not computed. For
          details, see 'qvalue.cal'.

_D_e_t_a_i_l_s:

     These parameters should only be changed if they are fully
     understood.

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

     A list containing the values of the parameters that are used in
     'sam' or 'ebam', respectively.

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

     Holger Schwender, holger.schwender@udo.edu

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

     Efron, B., Tibshirani, R., Storey, J.D. and Tusher, V. (2001).
     Empirical Bayes Analysis of a Microarray Experiment. _JASA_, 96,
     1151-1160.

     Schwender, H., Krause, A., and Ickstadt, K. (2006). Identifying
     Interesting Genes with siggenes. _RNews_, 6(5), 45-50.

     Storey, J.D. and Tibshirani, R. (2003). Statistical Significance
     for Genome-Wide Studies. _Proceedings of the National Academy of
     Sciences_, 100, 9440-9445.

     Tusher, V.G., Tibshirani, R., and Chu, G. (2001). Significance
     analysis of microarrays applied to the ionizing radiation
     response. _PNAS_, 98, 5116-5121.

_S_e_e _A_l_s_o:

     'limma2sam', 'limma2ebam', 'sam', 'ebam'

