CustomsTissue          package:XhybCasneuf          R Documentation

_C_u_s_t_o_m-_m_a_d_e _C_D_F'_s _p_r_o_b_e _s_e_t _p_a_i_r_s

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

     Custom-made CDF's probe set pairs

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

     data(CustomsTissue)
     data(CustomsTissueMC)
     data(CustomsTissue.noBl)

_F_o_r_m_a_t:

     These three data.frames contain data for the custom-made 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 'peCC' column holds the pairs'
     Pearson correlation coefficient calculated  on their expression
     intensities in the Tissue dataset (data originally from
     AtgenExpress Project).

     'CustomsTissue' is data.frame that contains all custom-made CDF's
     probe set pairs  with Q75 >= 55. 'CustomsTissueMC' holds a subset
     of the pairs in 'CustomsTissue', namely those whose
     metacorrelation coefficient is not NA are included.  For
     'CustomsTissue.noBl', the pairs of 'CustomsTissue' 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.c.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:

     'AffysTissue'

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

     data(CustomsTissue)
     data(CustomsTissueMC)
     data(CustomsTissue.noBl)

     ## see also the vignette

