estimerrors              package:rHVDM              R Documentation

_c_o_m_p_u_t_e_s _t_h_e _s_t_a_n_d_a_r_d _d_e_v_i_a_t_i_o_n _o_f _t_h_e _m_e_a_s_u_r_e_m_e_n_t _e_r_r_o_r _u_s_i_n_g _p_r_e-_c_a_l_c_u_l_a_t_e_d _t_a_b_l_e_s _s_p_e_c_i_f_i_c _t_o _t_h_e _p_l_a_t_t_f_o_r_m _o_r _u_s_e_r-_d_e_f_i_n_e_d _t_a_b_l_e

_D_e_s_c_r_i_p_t_i_o_n:

     This method takes as main input and ExpressionSet object, and
     using pre-calculated tables contained in rHVDM, it returns the
     same object with an extra slot that contains the standard
     deviation of the measurement error which is indispensable to then
     run rHVDM proper. The table can be user-defined. To check which
     tables are stored in rHVDM, just run the command without arguments
     ('estimerrors()'), it will return a list of the supported rHVDM
     plattforms. All parameters of this function are optional, see
     below for details on the effect of omitting one or more of them.
     The method assumes the the amount of error is dependent both on
     the particular microarray and the signal intensity. For more
     details on how it is computed, please refer to the  textual
     description of rHVDM.

_U_s_a_g_e:

     estimerrors(eset,plattid,refchips,errtable)

_A_r_g_u_m_e_n_t_s:

    eset: an object of class ExpressionSet (Biobase), every time this
          parameter is omitted the function returns a list of supported
          plattforms (identifier+plattform description). 

 plattid: an optional argument (character format) allowing to specify
          the plattform identifiers. These identifiers are rHVDM
          specific. Any identifier will be overriden by a table given
          as input of the 'errtable' argument. In future versions of
          rHVDM, if this argument and the 'errtable' are missing, a
          search will be done among the supported plattforms to find a
          matching plattform, based on the individual genes
          identifiers. For now, omission of both arguments will be
          conductive to outputting a list of supported plattforms. 

refchips: a vector of names or column indexes compatible with the
          ExpressionSet useds (note that this compatibility is not
          verified by the function, it is up to the user to supply
          compatible array names). Some microarray might be known to be
          of not very good quality and although the measurement error
          will be computed for these chips it is better to leave them
          out of early stages of the computation. The list to be input
          should typically contain the least noisy microarrays. This
          parameter is optional and if omitted, all microarrays are
          used. 

errtable: a nx2 table in matrix format. The first column of the matrix
          should contain reference log of signals in ascending order
          and the second the variance corresponding to the signals. 

_D_e_t_a_i_l_s:

     Local interpolation and individual array normalisation are used to
     estimate the standard deviation of the measurement error for each
     individual transcript on each microarray. The precise method is
     laid out in the paper cited below, with some minor modifications.

_V_a_l_u_e:

     Normally an updated eset is returned. In case some crucial element
     is missing, the original eset is returned. If the latter is
     missing too a list of supported plattform is returned (thus, when
     using this function, it is better to be careful of what lies at
     the LHS of the assignement arrow).

_N_o_t_e:

     The HTML report is generated in the working directory.

_A_u_t_h_o_r(_s):

     Martino Barenco

_R_e_f_e_r_e_n_c_e_s:

     M. Barenco, D. Tomescu, D. Brewer, R. Callard, J. Stark, M. Hubank
     (2006) Ranked predictions of p53 targets using Hidden Variable
     Dynamic Modelling. _Genome Biology_, *V7(3)*, R25.

_S_e_e _A_l_s_o:

     'HVDMcheck','training','screening','fitgene'

_E_x_a_m_p_l_e_s:

     data(HVDMexample)
     data(plattforms)
     fiveGybis<-estimerrors(eset=fiveGyMAS5,plattid="affy_HGU133A",refchips=leastnoisychips)
     #leastnoisy chips is a list of three chips identifiers stored in the HVDMexample data bundle

