oligo-package             package:oligo             R Documentation

_T_h_e _o_l_i_g_o _p_a_c_k_a_g_e: _a _t_o_o_l _f_o_r _a_n_a_l_y_s_i_s _o_f _o_l_i_g_o_n_u_c_l_e_o_t_i_d_e _a_r_r_a_y_s

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

     The 'oligo' package handles oligonucleotide arrays: expression,
     tiling, SNP and exon chips. The supported manufacturers are
     Affymetrix and NimbleGen. The package provides tools for
     preprocessing.

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

     The package will read the raw intensity files (CEL for Affymetrix;
     XYS for NimbleGen) and allow the user to perform analyses starting
     at the feature-level.

     Reading in the intensity files require the existence of data
     packages that contain the chip specific information (X/Y
     coordinates; feature types; sequence). These data packages
     packages are build using the 'makePlatformDesign' package, except
     for the Affymetrix SNP arrays that uses the data packages built
     via 'pdInfoBuilder' package. Soon, all the data packages will be
     built using the 'pdInfoBuilder' package.

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

     Benilton Carvalho - bcarvalh@jhsph.edu

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

     Carvalho, B.; Bengtsson, H.; Speed, T. P. & Irizarry, R. A.
     Exploration, Normalization, and Genotype Calls of High Density
     Oligonucleotide SNP Array Data. Biostatistics, 2006.

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

     ## rawData <- read.celfiles(list.celfiles())
     ## preProc <- snprma(rawData)
     ## gtCalls <- crlmm(preProc, correctionFile="outEM.rda")

