doPlotEset              package:ABarray              R Documentation

_P_r_o_d_u_c_e _a _n_u_m_b_e_r _o_f _Q_A _p_l_o_t _p_l_u_s _t _a_n_d _A_N_O_V_A _t_e_s_t

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

     Produce boxplot, MA plot, scatter plot, correlation, S/N detection
     concordance, CV, and t test, ANOVA test if subgroup is more than 2

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

     doPlotEset(eset, group, name = "", snThresh = 3, test = TRUE, ...)

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

    eset: an 'ExpressionSet' object

   group: name of the group from experiment design file

    name: a name for use in output files for record purpose

snThresh: threshold of S/N considered detectable, default = 3

    test: whether t or ANOVA test should be performed

     ...: Additional arguments, currently not implemented

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

     The t test and fold change is performed with function 'fctPlot'.
     See additional information with 'fctPlot'. ANOVA is performed with
     'doANOVA'.

     If there are more than 2 subgroup in 'group', t test and fold
     change will be performed for each pair of subgroup and one way
     ANOVA will be performed. If subgroup is 2, ANOVA will not be
     performed.

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

     None. A number of plots and t or ANOVA test result file will be
     produced.

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

     Y Andrew Sun

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

     #-doPlotEset(eset, "sampleGroup")
     #-doPlotEset(eset, "sampleGroup", name = "perfect")
     #-doPlotEset(eset, "sampleGroup", test = FALSE)  ##- t test will be not performed

