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 (Submitted) ;  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

