AffyRNAdeg               package:affy               R Documentation

_F_u_n_c_t_i_o_n _t_o _a_s_s_e_s_s _R_N_A _d_e_g_r_a_d_a_t_i_o_n _i_n _A_f_f_y_m_e_t_r_i_x _G_e_n_e_C_h_i_p _d_a_t_a.

_D_e_s_c_r_i_p_t_i_o_n:

     Uses ordered probes in probeset to detect possible RNA
     degradation. Plots and statistics used for evaluation.

_U_s_a_g_e:

     AffyRNAdeg(abatch,log.it=TRUE)
     summaryAffyRNAdeg(rna.deg.obj,signif.digits=3)
     plotAffyRNAdeg(rna.deg.obj, transform = "shift.scale", cols = NULL,
                      ...)

_A_r_g_u_m_e_n_t_s:

  abatch: An object of class 'AffyBatch-class'.

  log.it: A logical argument: If log.it=T, then probe data is log2
          tranformed

rna.deg.obj: Output from AffyRNAdeg

signif.digits: Number of significant digits to show.

transform: Possible choices are "shift.scale","shift.only", and
          "neither".  "Shift" vertically staggers the plots for
          individual chips, to make the display easier to read. "Scale"
          normalizes so that standard deviation is equal to 1.    

    cols: A vector of colors for plot, length = number of chips

     ...: further arguments for 'plot' function.

_D_e_t_a_i_l_s:

     Within each probeset, probes are numbered directionally from the
     5' end to the 3' end. Probe intensities are averaged by probe
     number, across all genes.   If log.it='FALSE' and
     transform="Neither", then  plotAffyRNAdeg  simply shows these
     means for each chip.  Shifted and scaled versions of the plot can
     make it easier to see.

_V_a_l_u_e:

     'AffyRNAdeg' returns a list with the following components: 

sample.names : names of samples, derived from affy batch object

means.by.number: average intensity by probe position

     ses: standard errors for probe position averages

   slope: from linear regression of means.by.number

  pvalue: from linear regression of means.by.number

_A_u_t_h_o_r(_s):

     Leslie Cope

_E_x_a_m_p_l_e_s:

     if (require(affydata)) {
       data(Dilution)
       RNAdeg<-AffyRNAdeg(Dilution)
       plotAffyRNAdeg(RNAdeg)
     }

