tstatistics              package:OCplus              R Documentation

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

     'tstatistics' computes either two-sample or paired t-statistics
     for a bunch of variables measured on the same objects, e.g.
     genewise t-statistics for a microarray experiment. 'PermNull' uses
     'tstatistics' to generate a permutation distribution.

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

     tstatistics(xdat, grp, logse = FALSE, paired = FALSE)

     PermNull(xdat, grp, nperm = 100, seed = NULL, logse = FALSE, paired=FALSE)

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

    xdat: the matrix of expression values, with genes (or variables) as
          rows and samples as columns.

     grp: a grouping variable giving the class membership of each
          sample, i.e. each column in 'xdat', see Details.

   nperm: number of permutations for establishing the null distribution
          of the t-statistic

    seed: random number generator seed for initializing the
          permutations from a known starting point.

   logse: logical flag indicating whether to return the logarithmized
          standard errors, too.

  paired: indicates whether to use two-sample or paired t-statistic.

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

     'tstatistics'  is a fairly fast replacement for function
     'mt.teststat' in package 'multtest', which is written exlusively
     in R and does not require loading half the Bioconductor
     infrastructure packages before doing anything. As such, it is used
     for computing the default test statistics by 'fdr1d' and 'fdr2d'.

     Note that for the paired test, 'tstatistics' requires the same
     data structure as 'mt.teststat': columns belonging to the same
     pair must be consecutive (though not necessarily in the same order
     throughout, as 'grp' will indicate the order). The function checks
     for this and barfs if it does not hold.

     'PermNull' returns the t-statistics and optionally the
     logarithmized standard errors of the mean for a specified number
     of permutations.

     Both functions are not especially economic in using memory, and
     collecting the whole set of permutations like 'PermNull' does
     instead of binning and counting them directly as they come is
     inherently wasteful.

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

     A data frame with first column 'tstat' and optionally (if
     'logse=TRUE') a second column 'logse'. 'tstat' returns the same
     number of test statistics as  rows in 'xdat' and in the same
     order, 'PermNull' does the same for consecutive permuations of the
     grouping variable 'grp'. 

     If the argument 'seed' is specified, 'PermNull' adds an attribute
     of the same name to the returned data frame.

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

     A. Ploner

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

     'fdr1d', 'fdr2d', examples in 'tMixture'

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

