limma2sam              package:siggenes              R Documentation

_l_i_m_m_a _t_o _S_A_M _o_r _E_B_A_M

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

     Transforms the output of an analysis with 'limma' into a 'SAM' or
     'EBAM' object, such that a SAM or EBAM analysis, respectively, can
     be performed using the test statistics provided by 'limma'.

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

     limma2sam(fit, coef, moderate = TRUE, sam.control = samControl())

     limma2ebam(fit, coef, moderate = TRUE, delta = 0.9, 
        ebam.control = ebamControl())

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

     fit: an object of class 'MArrayLM', i.e. the output of the
          functions 'eBayes' and 'lmFit' from the 'limma' package.

    coef: column number or name corresponding to the coefficient or
          contrast of interest. For details, see the argument 'coef' of
          the function 'topTable' in 'limma'.

moderate: should the 'limma' t-statistic be considered? If 'FALSE', the
          ordinary t-statistic is used in the trasnsformation to a
          'SAM' or 'EBAM' object. If 'TRUE', it is expected that 'fit'
          is the output of 'eBayes'. Otherwise, 'fit' can be the result
          of 'lmFit' or 'eBayes'.

sam.control: further arguments for the SAM analysis. See 'samControl'
          for these arguments, which should only be changed if they are
          fully understood.

   delta: the minimum posterior probability for a gene to be called
          differentially expressed (or more generally, for a variable
          to be called significant) in an EBAM analysis. For details,
          see 'ebam'. Please note that the meaning of  'delta' differs
          substantially between 'sam' and 'ebam'

ebam.control: further arguments for an EBAM analysis. See 'ebamControl'
          for these arguments, which should only be changed if their
          meaning is fully understood.

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

     An object of class 'SAM' or 'EBAM'.

_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.

     Smyth, G.K. (2004). Linear Models and Empirical Bayes Methods for
     Assessing Differential  Expression in Microarray Experiments.
     _Statistical Applications in Genetics and Molecular Biology_,
     3(1), Article 3.     

     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:

     'sam', 'ebam', 'SAM-class', 'EBAM-class', 'samControl',
     'ebamControl'

