rma                   package:affy                   R Documentation

_R_o_b_u_s_t _M_u_l_t_i-_A_r_r_a_y _A_v_e_r_a_g_e _e_x_p_r_e_s_s_i_o_n _m_e_a_s_u_r_e

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

     This function converts an 'AffyBatch' into an 'ExpressionSet'
     using the robust multi-array average (RMA) expression measure.

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

     rma(object,subset=NULL, verbose=TRUE, destructive = TRUE,normalize=TRUE,background=TRUE,bgversion=2,...)

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

  object: an 'AffyBatch'

  subset: a character vector with the the names of the probesets to be
          used in expression calculation.

 verbose: logical value. If 'TRUE' it writes out some messages
          indicating progress. If 'FALSE' nothing should be printed.

destructive: logical value. If 'TRUE' works on the PM matrix in place
          as much as possible, good for large datasets.

normalize: logical value. If 'TRUE' normalize data using quantile
          normalization

background: logical value. If 'TRUE' background correct using RMA
          background correction

bgversion: integer value indicating which RMA background to use 1: use
          background similar to pure R rma background given in affy
          version 1.0 - 1.0.2 2: use background similar to pure R rma
          background given in affy version 1.1 and above

     ...: further arguments to be passed (not currently implemented -
          stub for future use)

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

     This function computes the RMA (Robust Multichip Average)
     expression measure described in Irizarry et al Biostatistics
     (2003).

     Note that this expression measure is given to you in log base 2
     scale. This differs from most of the other expression measure
     methods.

     Please note that the default background adjustment method was
     changed during the lead up to the bioconductor 1.2 release. This
     means that this function and 'expresso' should give results that
     directly agree.

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

     An 'ExpressionSet'

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

     Ben Bolstad bmb@bmbolstad.com

_R_e_f_e_r_e_n_c_e_s:

     Rafael. A. Irizarry, Benjamin M. Bolstad, Francois Collin, Leslie
     M. Cope, Bridget Hobbs and Terence P. Speed (2003), Summaries of
     Affymetrix GeneChip probe level data Nucleic Acids Research
     31(4):e15

     Bolstad, B.M., Irizarry R. A., Astrand M., and Speed, T.P. (2003),
     A Comparison of Normalization Methods for High Density
     Oligonucleotide Array Data Based on Bias and Variance.
     Bioinformatics 19(2):185-193

     Irizarry, RA, Hobbs, B, Collin, F, Beazer-Barclay, YD, Antonellis,
     KJ, Scherf, U, Speed, TP (2003) Exploration, Normalization, and
     Summaries of High Density Oligonucleotide Array Probe Level Data.
     Biostatistics .Vol. 4, Number 2: 249-264

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

     'expresso'

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

     if (require(affydata)) {
       data(Dilution)
       eset <- rma(Dilution)
     }

