doPlotFCT              package:ABarray              R Documentation

_C_a_l_c_u_l_a_t_e _f_o_l_d _c_h_a_n_g_e _a_n_d _t _t_e_s_t, _t_h_e _p_l_o_t

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

     Calculate fold changes and p values from t test, and plot the
     results using preset FDR threshold

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

     doPlotFCT(eset, group, grpMember, order1 = NULL, order2 = NULL,
     detectSample = 0.5, snThresh = 3, ...)

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

    eset: an 'ExpressionSet' object

   group: which group from experiment design should calculation and
          plot be performed

grpMember: optional group member within the group

  order1: optional, For a pairwise comparison the ordering of the first
          group of replicates

  order2: optional, For a pairwise comparison the ordering of the first
          group of replicates

detectSample: optional number between 0 and 1 to indicate the
          percentage of arrays should be above snThresh to include in
          the t test analysis. Default = 0.5. If the probe is detected
          in 50% or more samples on one of the subgroup, the probe is
          included in the t test, otherwise, it will be excluded in the
          t test

snThresh: optional S/N ratio threshold. Default = 3

     ...: Additional argument, currently not implemented

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

     Group members are optional. For example, if group name is
     "tissue", and group members in experiment design file include
     "brain", "liver", "lung", "muscle". We could include c("brain",
     "liver") as group member for the parameter, then t test will be
     performed between "brain" and "liver", and "lung" "muscle" will be
     ignored. However, if we omit group member in the arguments, all
     tissue members will be used for t test. In this case, there will
     be 6 pairwise t test between each member of the group.

     If order1 and order2 are specified then a paired sample t-test
     will be conducted between the groups, with the arrays in each
     group sorted according to the ordering specified. For example, if
     order1 is c(1,3,2) and order2 is c(1,2,3), then the sample pairing
     is a1-b1, a3-b2, a2-b3, with a and b are subgroup 1 and subgroup 2
     within the group.

     The fold changes are difference between averaged subgroup1
     expression vs averaged subgroup2. If paired t test is performed,
     the fold changes are calculated using each paired difference and
     take an average of paired difference.

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

     None. But a number of plot and result files will be produced.

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

     Y Andrew Sun

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

     #- doPlotFCT(eset, "sampleGroup", c("liver", "muscle"))
     #- For a paired t test
     #- doPlotFCT(eset, "sampleGroup", c("liver", "muscle"), order1 = c(1,2,3), order2 = c(1,3,2))

