simpleaffy-deprecated       package:simpleaffy       R Documentation

_D_o_e_s _s_i_m_p_l_e_a_f_f_y _h_a_v_e _a _Q_C _d_e_f_i_n_i_t_i_o_n _f_i_l_e _f_o_r _t_h_e _s_p_e_c_i_f_i_e_d _a_r_r_a_y?

_D_e_s_c_r_i_p_t_i_o_n:

     The underlying implementation of simpleaffy has changed
     significantly and it now represents QC parameters differently. In
     particular, it loads only the QC data for the specified array
     type. A call to any of these functions loads the appropriate
     environment specifed by 'name'. They therefore been deprecated and
     WILL disappear from simpleaffy in the future.

_U_s_a_g_e:

       getTao(name)
       getAlpha1(name)
       getAlpha2(name)
       getActin3(name)
       getActinM(name)
       getActin5(name)
       getGapdh3(name)
       getGapdhM(name)
       getGapdh5(name)
       getAllQCProbes(name)
       getBioB(name)
       getBioC(name)
       getBioD(name)
       getCreX(name)
       getAllSpikeProbes(name)
       haveQCParams(name)

_A_r_g_u_m_e_n_t_s:

    name: The 'clean' CDF name of the array (i.e. the result of calling
          'cleancdfname' on the 'cdfName' of the AffyBatch object
          containing the array data of interest.

_D_e_t_a_i_l_s:

     Each of these functions has been replaced by a new function of the
     form 'qc.get.'. In order to support ratios other than gapdh and
     beta-actin, the appropriate way to get ratios is now to use
     'qc.get.ratios', which will return a table containing all
     suggested ratio calculations for the array. Similarly,
     'qc.get.spikes' will return a table containing all spike probesets
     for the array.

     One of the reasons for these changes is to make it easier to
     support new/alternate definitions of the QC parameters for a given
     array. The old functions do not know how to deal with alternate QC
     data from outside the package. 

     They have been left in, but deprecated - instead the new
     qc.get.X() functions should be used to pick up the additional
     functionality provided by, for example, the ability to use
     setQCEnvironment() to specify alternate QC definition files.

_V_a_l_u_e:

_N_o_t_e:

_A_u_t_h_o_r(_s):

     Crispin J Miller

_R_e_f_e_r_e_n_c_e_s:

     http://bioinformatics.picr.man.ac.uk/

_S_e_e _A_l_s_o:

     'setQCEnvironment' 'qc' 'qc.ok' 'cdfName' 'cleancdfname'
     'qc.get.ratios' 'qc.get.spikes' 'qc.get.probes'

_E_x_a_m_p_l_e_s:

       #old
       getBioB("hgu133plus2cdf")
       getActin3("hgu133plus2cdf")
       getActinM("hgu133plus2cdf")
       getActin5("hgu133plus2cdf")
       #new
       setQCEnvironment("hgu133plus2cdf")
       qc.get.spikes()["bioB"]
       r <- qc.get.probes()
       r["actin3"]
       r["actinM"]
       r["actin5"]