neg.contr               package:nudge               R Documentation

_I_n_d_i_c_a_t_o_r _o_f _k_n_o_w_n _t_r_u_l_y _n_o_n _d_i_f_f_e_r_e_n_t_i_a_l_l_y _e_x_p_r_e_s_s_e_d _g_e_n_e_s _i_n _t_h_e _h_i_v _d_a_t_a_s_e_t

_D_e_s_c_r_i_p_t_i_o_n:

     The ``hiv'' section of this dataset consists of cDNA from CD4+ T
     cell lines at 1 hour after infection with HIV-1BRU. There are 4608
     genes' expression levels. There are four replicates with balanced
     dye sways i.e. two of the replicates have sample 1 labeled with
     red and sample 2 labeled with green and the other two have the
     opposite labeling scheme. It is useful in testing the specificity
     of methods identifying differentially expressed genes, since there
     are 29 genes known not to be differentially expressed (non-human
     genes), called negative controls, identified in the vector of
     logical values ``neg.contr''.

_U_s_a_g_e:

     data(hiv)

_F_o_r_m_a_t:

     A logical vector containing 4608 indicators of known non
     differential expression

_S_o_u_r_c_e:

     Bumgarner Lab

_R_e_f_e_r_e_n_c_e_s:

     N. Dean and A. E. Raftery (2005). Normal uniform mixture
     differential gene expression detection for cDNA microarrays. BMC
     Bioinformatics. 6, 173-186.

     <URL: http://www.biomedcentral.com/1471-2105/6/173>

     A.B. van't Wout, G. K. Lehrma, S. A. Mikheeva, G. C. O'Keeffe, M.
     G. Katze, R. E. Bumgarner, G. K. Geiss and J. I. Mullins (2003).
     Cellular gene expression upon human immunodeficiency virus type 1
     infection of CD4+ T-Cell lines. J. Virol. 77, 1392-1402.

_S_e_e _A_l_s_o:

     'pos.contr','hiv'

