arrayWeights              package:limma              R Documentation

_A_r_r_a_y _Q_u_a_l_i_t_y _W_e_i_g_h_t_s

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

     Estimates relative quality weights for each array in a multi-array
     experiment with replication.

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

     arrayWeights(object, design = NULL, weights = NULL, method = "genebygene", maxiter = 50, tol = 1e-10, trace=FALSE)
     arrayWeightsSimple(object, design = NULL, maxiter = 100, tol = 1e-6, maxratio = 100, trace=FALSE)

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

  object: object of class 'numeric', 'matrix', 'MAList', 'marrayNorm',
          'exprSet' or 'PLMset' containing log-ratios or log-values of
          expression for a series of microarrays.

  design: the design matrix of the microarray experiment, with rows
          corresponding to arrays and columns to coefficients to be
          estimated.  Defaults to the unit vector meaning that the
          arrays are treated as replicates.

 weights: optional numeric matrix containing prior weights for each
          spot.

  method: character string specifying the estimating algorithm to be
          used. Choices are '"genebygene"' and '"reml"'.

 maxiter: maximum number of iterations allowed.

     tol: convergence tolerance.

maxratio: maximum ratio between largest and smallest weights before
          iteration stops

   trace: logical variable. If true then output diagnostic information
          at each iteration of '"reml"' algorithm.

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

     The relative reliability of each array is estimated by measuring
     how well the expression values for that array follow the linear
     model.

     A heteroscedastic model is fitted to the expression values for 
     each gene by calling the function 'lm.wfit'.  The dispersion model
      is fitted to the squared residuals from the mean fit, and is set
     up to  have array specific coefficients, which are updated in
     either full REML  scoring iterations, or using an efficient
     gene-by-gene update algorithm.   The final estimates of these
     array variances are converted to weights.

     The data object 'object' is interpreted as for 'lmFit'. In
     particular, the arguments 'design' and 'weights' will be extracted
     from the data  'object' if available and do not normally need to
     be set explicitly in  the call; if any of these are set in the
     call then they will over-ride  the slots or components in the data
     'object'.

     'arrayWeightsSimple' is a fast version of 'arrayWeights' with
     'method="reml"', no prior weights and no missing values.

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

     A vector of array weights.

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

     Matthew Ritchie and Gordon Smyth

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

     Ritchie, M. E., Diyagama, D., Neilson, van Laar, R., J., Dobrovic,
     A., Holloway, A., and Smyth, G. K. (2006). Empirical array quality
     weights for microarray data. BMC Bioinformatics. (Accepted 11
     April 2006)

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

     An overview of linear model functions in limma is given by
     06.LinearModels.

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

     library(sma)
     # Subset of data from ApoAI case study in Limma User's Guide
     data(MouseArray)
     # Avoid non-positive intensities
     RG <- backgroundCorrect(mouse.data, method="half")
     MA <- normalizeWithinArrays(RG, mouse.setup)
     MA <- normalizeBetweenArrays(MA, method="Aq")
     targets <- data.frame(Cy3=I(rep("Pool",6)),Cy5=I(c("WT","WT","WT","KO","KO","KO")))
     design <- modelMatrix(targets, ref="Pool")
     arrayw <- arrayWeightsSimple(MA, design)
     fit <- lmFit(MA, design, weights=arrayw)
     fit2 <- contrasts.fit(fit, contrasts=c(-1,1))
     fit2 <- eBayes(fit2)
     # Use of array weights increases the significance of the top genes
     topTable(fit2)

