lumiT                  package:lumi                  R Documentation

_T_r_a_n_s_f_e_r _t_h_e _I_l_l_u_m_i_n_a _d_a_t_a _t_o _s_t_a_b_i_l_i_z_e _t_h_e _v_a_r_i_a_n_c_e

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

     Transfer the Illumina data to stabilize the variance.

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

     lumiT(x.lumi, method = c("vst", 'log2', 'cubicRoot'), ifPlot = FALSE, simpleOutput = TRUE, ...)

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

  x.lumi: LumiBatch object 

  method: four methods are supported: "vst", "log2", "cubicRoot" 

  ifPlot: determine whether to plot the intermediate results 

simpleOutput: determine whether to simplify the output LumiBatch
          object, which will set the se.exprs, detection and beadNum
          slots as NULL. 

     ...: other parameters used by 'vst' 

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

     lumiT is an interface of difference variance stabilizing
     transformation. See 'vst' for details of VST (Variance Stabilizing
     Transform) of Illumina data.

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

     Return a LumiBatch object with transformed expression values. It
     also includes the VST transform function and its parameters as
     attributes: "transformFun", "parameter". See 'inverseVST' for
     details.

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

     Pan Du, Simon Lin

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

     Lin, S.M., Du, P., Kibbe, W.A.,  {\it Model-based
     Variance-stabilizing Transformation for Illumina Microarray Data},
     submitted

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

     'vst'

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

     ## load example data
     data(example.lumi)

     ## Do default VST variance stabilizing transform
     lumi.T <- lumiT(example.lumi, ifPlot=TRUE)

