dd             package:Agi4x44PreProcess             R Documentation

_d_a_t_a _e_x_a_m_p_l_e (_R_G_L_i_s_t)

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

     Data, extracted from scanned images using Agilent Feature
     Extraction Software, are stored in a RGList object.  This example
     includes 2 experimental conditions. Two replicates are considered

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

     data(dd)

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

     A data example is provided, in which the original data have been
     trimmed  to reduced the disk space storing. As a consequence, some
     of the functions regarding countint replicated probes, etc., will
     produce numbers that will not coincide with a 'real data'. Despite
     of this, the example is valid  to illustrate all the function
     features of the functions included in the package.

     Chips were scanned using the Agilent G2567AA Microarray Scanner
     System (Agilent Technologies) with the extended dynamic range
     option turned on. Image analysis and data collection were carried
     out using the Agilent Feature Extraction 9.1.3.1. (AFE). For the
     background signal calculation the AFE was set to use the spatial
     detrend surface value that estimate the noise due to a systematic
     gradient on the array and whose computation is based on a Loess
     algorithm. Details of how the spatial detrend algorithm works can
     be found in the AFE reference guide.

     Data, colected with the Agilent Feature Extraction Software, are
     stored in a RGList object with the following components:  - dd$R: 
                           'gProcessedSignal' - dd$G:                  
          'gMeanSignal' - dd$Rb:                      
     'gBGMedianSignal'  - dd$Gb:                       'gBGUsed'  -
     dd$targets                   'targets' - dd$genes$ProbeName       
       'Probe Name' - dd$genes$GeneName           'Gene Name' -
     dd$genes$SystematicName     'Systematic Name' -
     dd$genes$Description        'Description Name ' -
     dd$genes$Sequence           '60 bases Sequence' -
     dd$genes$ControlType        'FLAG to specify the sort of feature'
     - dd$other$gIsWellAboveBG     'FLAG IsWellAboveBG' -
     dd$other$gIsFound           'FLAG IsFound' - dd$other$gIsSaturated
           'FLAG IsSaturated' - dd$other$gIsFeatPopnOL      'FLAG
     IsFeatPopnOL' - dd$other$gIsFeatNonUnifOL   'FLAG IsFeatNonUnifOL'
     - dd$other$chr_coord         'CHR coordinate (obtained from
     Agilent data files) Later, the if an annotation package exists,
     the fields 'SystematicName', 'GeneName'  and 'Description' are
     replaced, respectively,  by the corresponding ACCNUM, SYMBOL  and
     DESCRIPTION obtained from the annotation package.

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

     code{read.targets} code{targets}

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

     ## Not run: 
             data(dd)
             head(data)
     ## End(Not run)

