createBeadSummaryData       package:beadarray       R Documentation

_P_r_o_d_u_c_e _b_e_a_d _a_v_e_r_a_g_e_s

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

     Produce bead averages for each bead type used in an experiment on
     a specified set of arrays.

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

     createBeadSummaryData(BLData, log=FALSE, n=3,
                    imagesPerArray = 2, probes = NULL)

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

  BLData: an BeadLevelList object

     log: if TRUE then summarise the log2 intensities of each bead

       n: use n median absolute deviations from the mean as a cut-off
          for outliers

imagesPerArray: Specifies how many images there are per array. Normally
          1 for a SAM and 2 for a BeadChip.  The images from the same
          array will be combined so each column in the output
          represents a sample 

  probes: Specify particular probes to summarise.  If left NULL then
          all the probes on the first array are used.

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

     Objects which are created seperately by 'createBeadSummaryData'
     may be joined by using the 'cbind' function.

     To summarise each bead type we first have to remove the outliers
     for the bead type on the array. The default method is the method
     used by Illumina which uses the raw (un-logged) intensities and
     categorises outliers as being those beads which have intensity
     more than 3 median absolute deviations from the bead mean
     intensity. By setting the log parameter we can use the log2
     intensities instead of un-logged and by setting the 'n' parameter
     we choose beads with intensity 'n' mads from the mean.

     With outliers removed, we simply take an average of the green (and
     red, if present) intensities of the remaining beads and create $G
     and $R matrices. We also store the number of outliers that were
     detected for each bead type and the standard error of the
     remaining beads in the '$GNoBeads' and '$GBeadStDev' (and
     '$RNoBeads' and '$RBeadStDev' for two-colour data) matrices
     respectively.

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

     An ExpressionSetIllumina (bead summary) object (or SnpSetIllumina
     object for two-colour data) in which all components (G,GBeadStDev
     ....) are matrices with number of rows equal to the number of bead
     types for the experiment and number of columns equal to the length
     of the 'arrays' object.

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

     Mark Dunning and Mike Smith

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

     'findBeadStatus'

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

     ##produce bead summaries for the first array in our BLData object
     #data(BLData)
     #BSData = createBeadSummaryData(BLData, log=TRUE)
     #names(BSData)

