getMDB                 package:maDB                 R Documentation

_R_e_t_r_i_e_v_i_n_g _r_e_g_u_l_a_t_i_o_n _v_a_l_u_e_s _f_r_o_m _a _d_a_t_a_b_a_s_e.

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

     'getMDB' this function reads the regulation (M) values from the
     selected comparisons out of a PostgreSQL database. Micro array
     experiments can be stored into a PostgreSQL database using the
     'publishToDB' method of the 'EexprSet' object. The corresponding
     regulation values can then be calculated with the
     'calculateDBRegulations' function.

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

     getMDB(con,ids=NULL,comparisons.pk=NULL,v=TRUE,column.names="description")

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

     con: A connection object (create it with the dbConnect.PgSQL.conn
          function from the package RdbiPgSQL)

     ids: The IDs of the genes from which the expression values should
          be retrieved. In the case of Affymetrix GeneChips the
          Affymetrix IDs should be used (as they are used as rownames
          in the 'exprs' matrix in the 'exprSet' objects).

comparisons.pk: the primary keys of the comparisons in the database
          from which the regulation values should be retrieved. To get
          all available comparisons from the database call
          'dbGetResult(dbSendQuery(con,"SELECT * FROM comparisons"))',
          where 'con' is the database connection object and the column
          'comparisons_pk' contains the primary keys. This SQL call can
          be extended to the samples that are hybridized in the signal
          channel used as "red" signal channel ('M = log2( R / G)'):
          'dbGetResult(dbSendQuery(con,"SELECT * FROM comparisons JOIN
          signal_channels ON (red_signal_channel=signal_channels_pk)
          JOIN samples ON (samples_fk=samples_pk)"))'. By switching the
          "red_signal_channel" with "green_signal_channel" the call
          retrieves the same information, but with information about
          the green signal channel (usually the control sample).

column.names: The information that should be used as column names of
          the returned regulation values matrix. Allowed are all column
          names of the sample and comparisons database tables.

       v: If TRUE additional information will be printed to the
          console.

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

     This function is useful, if one wants to get regulation values of
     a set of genes in a set of comparisons.

_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:

     'publishToDB' 'dbGetExperimentInfo' 'loadFromDB' 'getEDB'

