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 _l_o_w-_l_e_v_e_l _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 built using the 'pdInfoBuilder' package. 

     For Affymetrix SNP arrays, users are asked to download the already
     built annotation packages from BioConductor. This is because these
     packages contain metadata that are not (yet) automatically
     created. The following annotation packages are available:

     50K Xba  - pd.mapping50kxba.240 50K Hind - pd.mapping50khind.240
     250K Sty - pd.mapping250k.sty 250K Nsp - pd.mapping250k.nsp
     GenomeWideSnp 5 (SNP 5.0) - pd.genomewidesnp.5 GenomeWideSnp 6
     (SNP 6.0) - pd.genomewidesnp.6

     For users interested in genotype calls for SNP 5.0 and 6.0 arrays,
     we strongly recommend the use use the 'crlmm' package, which
     implements a more efficient version of CRLMM.

_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.

