selSpots             package:maigesPack             R Documentation

_S_e_l_e_c_t _s_p_o_t_s _t_o _u_s_e _i_n _n_o_r_m_a_l_i_s_a_t_i_o_n

_D_e_s_c_r_i_p_t_i_o_n:

     Function to select spots to be used in microarray normalisation.

_U_s_a_g_e:

     selSpots(obj=NULL, sigNoise=1, rmFlag=NULL, gLabelsID=c("Name"),
              remove=list(c("BLANK","DAP","LYS","PHE","Q_GENE","THR","TRP")),
              badSpots=NULL, badLabel=NULL)

_A_r_g_u_m_e_n_t_s:

     obj: object of class 'maigesRaw'.

sigNoise: positive real number indicating the cutoff to remove spots
          with signal-to-noise ratio below it.

  rmFlag: vector of flag symbols to be removed (for normalisation).
          These flags are stored in the slot 'Flags' from 'maigesRaw'
          class.

gLabelsID: character vector indicating the gene labels to be searched
          to exclude that ones specified in 'remove' argument.

  remove: list of same length as 'GlabelsID' containing character
          vector indicating the symbols of spots to be removed,
          according to the 'GlabelsID' argument.

badSpots: index of bad spots (numeric or logical) identifying bad
          spots. May be the gene labels, with label ID specified by the
          argument 'badLabel'.

badLabel: character string specifying the gene label ID for remove
          'badSpots'.

_D_e_t_a_i_l_s:

     This function takes the object of class 'maigesRaw' and actualise
     the slot 'UseSpots' according with the arguments passed to the
     function. This slot is read by the normalisation functions
     'normLoc', 'normOLIN', 'normRepLoess', 'normScaleLimma' and
     'normScaleMarray' to use only the spots that passed the criteria
     specified here.

_V_a_l_u_e:

     This function returns another object of class 'maigesRaw' with the
     'UseSpots' slot actualised.

_A_u_t_h_o_r(_s):

     Gustavo H. Esteves <gesteves@vision.ime.usp.br>

_E_x_a_m_p_l_e_s:

     ## Loading the dataset
     data(gastro)

     ## Filtering all spots with signal2noise ratio (Sf/Sb or Rf/Rb) greater
     ## or equal to 1 and that have 'Name' label as 'BLANK', 'DAP', ..., 'TRP'.
     gastro.raw2 = selSpots(gastro.raw, sigNoise=1, rmFlag=NULL, gLabelsID="Name",
       remove=list(c("BLANK","DAP","LYS","PHE","Q_GENE","THR","TRP")))

     ## To see the number of spots that suvived the filtering above do
     apply(gastro.raw2@UseSpots, 2, sum)

     ## To do the same filtering as above, also filtering flags marcke as 1
     ## and 4 do
     gastro.raw2 = selSpots(gastro.raw, sigNoise=1, rmFlag=c(1,4), gLabelsID="Name",
       remove=list(c("BLANK","DAP","LYS","PHE","Q_GENE","THR","TRP")))

     apply(gastro.raw2@UseSpots, 2, sum)

