ssStatistic               package:XDE               R Documentation

_C_a_l_c_u_l_a_t_e _s_i_n_g_l_e _s_t_u_d_y _e_s_t_i_m_a_t_e_s _o_f _e_f_f_e_c_t _s_i_z_e

_D_e_s_c_r_i_p_t_i_o_n:

     Calculate single study estimates of effect size for lists of
     'ExpressionSets'

_U_s_a_g_e:

     ssStatistic(statistic = c("t", "sam", "z")[1], phenotypeLabel, esetList, ...)

_A_r_g_u_m_e_n_t_s:

statistic: Character string indicating Welch t-statistic (t), SAM
          (sam), or a z-statistic (z)

phenotypeLabel: Character string indicating the name of the binary
          covariate

esetList: An object of class 'ExpressionSetList'

     ...: Not implemented. Potentially additional arguments to the
          above methods that are implemented in other packages

_D_e_t_a_i_l_s:

     This function is a wrapper that provides an estimate of effect
     size for each study (element) in an 'ExpressionSetList' object.

     For Welch t-statistic, this function is a wrapper for mt.teststat
     in the multtest package.

     For SAM, this function is a wrapper for the sam function in the
     siggenes package.

     The "z" statistic is a standardized unbiased estimate of effect
     size (Hedges and Olkin, 1985) - implementation is in the zScores
     function in the R package GeneMeta.

     See the complete references below.

_V_a_l_u_e:

     A matrix: rows are genes and columns are studies

_A_u_t_h_o_r(_s):

     R. Scharpf

_R_e_f_e_r_e_n_c_e_s:

     J.K. Choi, U. Yu, S. Kim, and O.J. Yoo (2003), Combining multiple
     microarray studies and modeling interstudy variation,
     Bioinformatics, 19(1) I84-I90.

     Y. Ge, S. Dudoit & T. P. Speed (2003), Resampling-based multiple
     testing for microarray data hypothesis Test 12(1) : 1-44 (with
     discussions on 44-77).

     L. Lusa R. Gentleman, and M. Ruschhaupt, GeneMeta: MetaAnalysis
     for High Throughput Experiments

     L.V. Hedges and I. Olkin, Statistical Methods for Meta-analysis
     (1985), Academic Press

     Tusher, Tibshirani and Chu (2001), Significance analysis of
     microarrays applied to the ionizing radiation response, PNAS 2001
     98: 5116-5121, (Apr 24).

_E_x_a_m_p_l_e_s:

     data(expressionSetList)
     if(require(multtest)){
       t <- ssStatistic("t", esetList=expressionSetList, phenotypeLabel="adenoVsquamous")
     }  

