dbCalculateRegulations         package:maDB         R Documentation

_C_a_l_c_u_l_a_t_e _r_e_g_u_l_a_t_i_o_n _v_a_l_u_e_s _f_r_o_m _e_x_p_r_e_s_s_i_o_n _v_a_l_u_e_s _i_n _t_h_e _d_a_t_a_b_a_s_e

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

     'dbCalculateRegulations' This function calculates regulation
     values from expresison values in the database and inserts the
     newly calculated regulation values in the according database
     table.

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

     dbCalculateRegulations(Con,exp.title,comparisons,v=TRUE)

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

     Con: The connection to the database (see 'dbConnect' from the
          'RdbiPgSQL' package).

exp.title: The tile of the micro array experiment for which the
          regulation values should be calculated. Note that it is only
          possible to calculate regulation values for comparisons of
          arrays within a micro array experiment, which means that this
          regulation values can only be calculated for arrays or
          Affymetrix GeneChips which were normalized together and their
          expression values have been adjusted between the arrays.

comparisons: A list of comparisons that should be calculated. To
          calculate regulation values for the first three chips of an
          experiment (comparing the expression values of the second
          chip with those of the first (control) and the same for the
          third) submit 'list(c(2,1),c(3,1))'. Use the function
          'dbGetExperimentInfo' to get the information at which index
          which sample is stored in the database.

       v: If 'TRUE' a progress bar will be drawn.

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

     This function allows to calculate regulation values comparing
     expression values from signal channels of an micro array
     experiment. The according comparisons will be inserted into a
     database table called 'comparisons' whichs attribute
     'r_signal_channel' links to the signal channel that was used as
     sample and whichs attribute 'g_signal_channel' links to the signal
     channel that was used as control sample. The regulation values are
     calculated using the formula 'M=r-g' and 'A=0.5*(r+g)' where 'r'
     and 'g' are the expression values in log2 scale. The regulation
     values (M and A values) are inserted into a database table called
     'regulation_values'. Regulation values can be fetched from the
     database using the 'getMDB' function. To get the information which
     samples were compared in the comparisons in the database the
     "samples" and "comparisons" can be joined (eg
     'dbSendQuery(con,"SELECT * FORM comparisons JOIN signal_channels
     ON (r_signal_channel=signal_channels_pk) JOIN samples ON
     (samples_fk=samples_pk)")' gets all comparisons from the database
     togehter with the information of which signal channel with which
     sample hybridized onto was used as "red" channel. By switching the
     "red_signal_channel" with "green_signal_channel" the same can be
     done for the "green" signal channel (usually the control sample in
     the formula 'M = log2(R/G)')).

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

     Johannes Rainer

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

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

     'dbGetExperimentInfo'

