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)
     }

