ddCt                  package:prada                  R Documentation

_A_p_p_l_y _t_h_e _d_d_C_t _m_e_t_h_o_d _f_o_r _a _g_i_v_e_n _d_a_t_a _s_e_t (_w_i_t_h _o_r _w_i_t_h_o_u_t _e_f_f_i_c_i_e_n_c_i_e_s

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

     Apply the ddCt method for a given data set

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

     ddCt(raw.table,calibrationSample,housekeepingGenes,type="mean",sampleInformation=NULL,filename="warning.output.txt")

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

raw.table: data frame. It must contain columns with the following
          names:'Ct','Sample','Detector','Platename'. The column 'Ct'
          must contain numeric values.

calibrationSample: character. Name of the calibration samples.

housekeepingGenes: character. Name of the housekeeping genes.

sampleInformation: if specified it must be an object of class
          'phenoData' with a column named 'Sample'.

filename: character of length 1. The name of the file the warnings
          should be stored in.

    type: character of length 1. `mean` or `median`- which method
          should be used for the aggregation of the repicates

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

     Please see vignette 'How to apply the ddCt method' in the ddCt
     package for details.

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

     A an object of class 'eSet'. Its eList has the following names:
     exprs(the level), level.err, Ct, Ct.error, dCt, dCt.error, ddCt,
     ddCt.error, Difference, number_NA, number, Plate.

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

     Markus Ruschhaupt <URL: mailto:m.ruschhaupt@dkfz.de>

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

     'readSDM','eListWrite'

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

     ##see vignette rtPCR.pdf

