CATPlots               package:applera               R Documentation

_C_A_T_p_l_o_t_s _i_s _a _q_u_a_l_i_t_y _c_o_n_t_r_o_l _f_u_n_c_t_i_o_n _t_o _e_v_a_l_u_a_t_e _r_e_p_l_i_c_a_t_e_s _q_u_a_l_i_t_y

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

     This function is used to evaluate the quality of biological
     replicates using the CAT plots originally develped by Irizarry in
     Nature Methods 2005. The function has been build for comparing
     replicate quality in a two groups experiment (e.g. test set vs
     reference set).

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

     CATPlots(object, cond, minGenes=25, maxGenes=1000, upsideDown=FALSE)

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

  object: An applera object, or an exprSet object or a matrix of
          expression values, where columns are arrays replicates and
          rows are genes.

    cond: A vector of 0 and 1, where 1 indicates the group of test
          arrays (Trt) to be evaluated with respect to a group of
          reference arrays (Ctrl) indicated by 0.

minGenes: Min number of genes to be used to create the gene lists. For
          more information see the applera vignette.

maxGenes: Max number of genes to be used to create the gene lists. For
          more information see the applera vignette.

upsideDown: A logical parameter that allows to perfome CATplots also on
          the reversed condition vector, where 0s are now 1s and 1s are
          0s.

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

     See applera vignette

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

     Results are represented as plots and the function returns a list. 

resultR2Trt : R-squared correlation among Trt data.

resultR2Crt : R-squared correlation among Ctrl data.

_N_o_t_e:

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

     Francesca Cordero <fcordero@di.unito.it>

_R_e_f_e_r_e_n_c_e_s:

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

     # data(test)
     # tmp1 <- exprs(signal(test))
     # tmp2 <- CATPlots(tmp1, c(0,0,0,1,1,1), 1, 1000, FALSE)

