AffysTissue           package:XhybCasneuf           R Documentation

_A_f_f_y_m_e_t_r_i_x' _C_D_F _p_r_o_b_e _s_e_t _p_a_i_r_s

_D_e_s_c_r_i_p_t_i_o_n:

     Affymetrix' CDF probe set pairs

_U_s_a_g_e:

     data(AffysTissue)
     data(AffysTissueMC)
     data(AffysTissue.noBl)

_F_o_r_m_a_t:

     These three data.frames contain data for Affymetrix' CDF's probe
     set pairs with Q75 >= 55. The 'pr' and 'target' columns hold the
     names of probe set X and Y, respectively.  Column 'alSum' contains
     the Q75 value of the alignment scores of X's  reporters to the
     transcript of Y.  The 'meant2hit' and 'PSofTarget' columns contain
     respectively the gene locus  the probe set was designed to target
     and the probe set ID of the off-target Y,  according to Affymetrix
     (extracted from ATH1-121501_annot.csv). The 'peCC' column holds
     the pairs' Pearson correlation coefficient calculated  on their
     expression intensities in the Tissue dataset (data originally from
     AtgenExpress Project).

     'AffysTissue' is data.frame that contains all Affymetrix' CDF's
     probe set pairs  with Q75 >= 55. 'AffysTissueMC' holds a subset of
     the pairs in 'AffysTissue', namely those whose metacorrelation
     coefficient is not NA are included.  For 'AffysTissue.noBl', the
     pairs of 'AffysTissue' that align to each  other with BLAST in at
     least one direction with an E-value smaller than 10^{-10} were
     omitted.

_A_u_t_h_o_r(_s):

     Tineke Casneuf tine@ebi.ac.uk

_R_e_f_e_r_e_n_c_e_s:

     Casneuf, Van de Peer and Huber,  AtgenExpress data used: Schmid,
     M., Davison, T. S., Henz, S. R., Pape, U. J., Demar, M., Vingron,
     M. Schoelkopf, B. Weigel, D., and Lohmann, J. (2005) A gene
     expression map of Arabidopsis development. _Nature Genetics_, 37,
     501-506.

_S_e_e _A_l_s_o:

     'CustomsTissue'

_E_x_a_m_p_l_e_s:

     data(AffysTissue)
     data(AffysTissueMC)
     data(AffysTissue.noBl)

     ## see also the vignette

