selectHKgenes             package:SLqPCR             R Documentation

_S_e_l_e_c_t_i_o_n _o_f _r_e_f_e_r_e_n_c_e/_h_o_u_s_e_k_e_e_p_i_n_g _g_e_n_e_s

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

     This function can be used to determine a set of
     reference/housekeeping (HK)  genes for gene expression
     experiments.

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

     selectHKgenes(relData, method = "Vandesompele", minNrHK = 2, geneSymbol, 
                   trace = TRUE, na.rm = FALSE)

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

 relData: matrix or data.frame containing relative expression values 

  method: method to compute most stable genes 

 minNrHK: minimum number of HK genes that should be considered 

geneSymbol: gene symbols 

   trace: logical, print additional information 

   na.rm: a logical value indicating whether 'NA' values should be
          stripped before the computation proceeds.  

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

     This function can be used to determine a set of
     reference/housekeeping (HK) genes for gene expression experiments.
     The default method '"Vandesompele"' was proposed by Vandesompele
     et al. (2002).

     Currently, only the method by Vandesompele et al. (2002) is
     implemented.

     Vandesompele et al. (2002) propose a cut-off value of 0.15 for the
      pairwise variation. Below this value the inclusion of an
     additional housekeeping gene is not required.

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

     If 'method = "Vandesompele"' a list with the following components
     is returnd 

ranking : ranking of genes from best to worst where the two most stable
          genes cannot be ranked 

variation : pairwise variation during stepwise selection 

  meanM : average expression stability M 

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

     Dr. Matthias Kohl (SIRS-Lab GmbH) kohl@sirs-lab.com

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

     Jo Vandesompele, Katleen De Preter, Filip Pattyn et al. (2002).
     Accurate  normalization of real-time quantitative RT-PCR data by
     geometric averaging  of multiple internal control genes.  Genome
     Biology 2002. 3(7):research0034.1-0034.11. <URL:
     http://genomebiology.com/2002/3/7/research/0034/>

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

     data(vandesompele)
     res.BM <- selectHKgenes(vandesompele[1:9,], method = "Vandesompele", geneSymbol = names(vandesompele), minNrHK = 2, trace = TRUE, na.rm = TRUE)

