rma                  package:oligo                  R Documentation

_R_M_A - _R_o_b_u_s_t _M_u_l_t_i_c_h_i_p _A_v_e_r_a_g_e _a_l_g_o_r_i_t_h_m

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

     Robust Multichip Average methodology. This will convert an
     (Expression/Exon/Gene)FeatureSet object to an ExpressionSet object
     by using RMA strategy.

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

     rma(object, ...)

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

  object: 'FeatureSet' object

     ...: Extra arguments.

_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.

     For Exon ST and Gene ST arrays, the user should be aware that the
     summarization is performed to the *probeset* level. The
     ExpressionSet returned when either Exon/Gene-FeatureSet objects
     are passed contain extra annotation on the featureData slot that
     the user should take into account for exon/gene-level analyses.

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

     'ExpressionSet' object.

_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), Summa ries 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 O
     ligonucleotide 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, Normalizati on, and
     Summaries of High Density Oligonucleotide Array Probe Level Data.
     Biostatistics .Vol. 4, Number 2: 249-264

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

     'snprma'

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

     if (require(maqcExpression4plex) & require(pd.hg18.60mer.expr)){
     xysPath <- system.file("extdata", package="maqcExpression4plex")
     xysFiles <- list.xysfiles(xysPath, full.name=TRUE)
     ngsExpressionFeatureSet <- read.xysfiles(xysFiles)
     summarized <- rma(ngsExpressionFeatureSet)
     show(summarized)
     }

