doProbeTTest         package:GeneRegionScan         R Documentation

_D_o _P_r_o_b_e _T-_T_e_s_t

_D_e_s_c_r_i_p_t_i_o_n:

     Internal function used to calculate t-tests between probe level
     intensity and pData entries with two levels.

_U_s_a_g_e:

         doProbeTTest(object, label, testType="students")

_A_r_g_u_m_e_n_t_s:

  object: A ProbeLevelSet object or a regular ExpressionSet object.

   label: An optional character string specifying a column name in the
          pData of the object. If this argument is given, the gene plot
          will be colour coded based on the different groups (factors)
          in the pData entry. If a summaryType other than 'dots' is
          selected the summarisation is done stratified by the
          different groups in the pData.

testType: Character string, defining a statistic procedure to identify
          especially interesting probes.

_D_e_t_a_i_l_s:

     This function is not meant to be called by the user. It does the
     statistical calculations when called by plotStatistics

_V_a_l_u_e:

     A correlation list with p-value and fold-change in columns and
     probe IDs as rownames. Used by plotStatistics when decorating
     plots from plotOnGene.

_A_u_t_h_o_r(_s):

     Lasse Folkersen

_S_e_e _A_l_s_o:

     'plotStatistics', 'plotOnGene'

_E_x_a_m_p_l_e_s:

             data(exampleProbeLevelSet)
             colnames(pData(exampleProbeLevelSet))
             tTestData<-GeneRegionScan:::doProbeTTest(exampleProbeLevelSet,"gender")
             colnames(tTestData)
             
             #P value for the probe with ID 679083 in relation to "gender"
             print(tTestData["679083","p-value"])

