fibroEset             package:fibroEset             R Documentation

_D_a_t_a _f_r_o_m _t_h_e _m_i_c_r_o_a_r_r_a_y _e_x_p_e_r_i_m_e_n_t _o_f _h_u_m_a_n, _b_o_n_o_b_o _a_n_d _g_o_r_i_l_l_a _c_u_l_t_u_r_e_d _f_i_b_r_o_b_l_a_s_t_s _d_o_n_e _b_y _K_a_r_a_m_a_n _e_t _a_l. (_2_0_0_3)

_D_e_s_c_r_i_p_t_i_o_n:

     Total RNA from early-passage primary fibroblast cell lines from 18
     human, 10 bonobo and 11 gorilla donors was extracted and
     gene-expression analysis performed using Affymetrix U95Av2.

_U_s_a_g_e:

     data(fibroEset)

_F_o_r_m_a_t:

     Expression set with 12625 genes and 46 samples. 
      There are 2 covariates listed.

        *  'samp': sample code.

        *  'species': The species the sample was obtained from. 
             h: human (Homo sapiens), b: bonobo (Pan paniscus), g:
           gorilla (Gorilla gorilla)

_D_e_t_a_i_l_s:

     Data preprocessing (as described in the publication): 
      The raw expression scores for every gene in every sample were
     generated using AFFYMETRIX GENECHIP 5.0. Normalization was done by
     calculating multiplicative scaling factors on the basis of the
     median intensity of the 60th to 95th percentile of gene-expression
     scores. All gene-expression scores below 100 were set to 100 to
     minimize noise associated with less robust measurements of rare
     transcripts.

     The usage of a human chip can cause mismatches between the ape RNA
     samples and human oligonucleotide probes. Because 16 perfect match
     probes interrogate each gene, the effect of mismatches should be
     minimal (Hacia et al. 1998).

_S_o_u_r_c_e:

     <URL: http://lichad.usc.edu/supplement/index.html>

_R_e_f_e_r_e_n_c_e_s:

     Karaman M.W., Houck M.L., Chemnick L.G., Nagpal S., Chawannakul
     D., Sudano D., Pike B.L., Ho V.V., Ryder O.A. & Hacia J.G. (2003)
     Comparative Analysis of Gene-Expression Patterns in Human and
     African Great Ape Cultured Fibroblasts. _Genome Research_ *13*,
     1619-1630.

     Hacia J.G. et al. (1998) Evolutionary sequence comparisons using
     high-density oligonucleotide arrays. _Nature genetics_ *18*,
     155-158.

_E_x_a_m_p_l_e_s:

     library(Biobase)
     data(fibroEset)
     xx <- exprs(fibroEset)
     colnames(xx) <- as.character(fibroEset$species)
     dim(xx)
     xx[1:5,1:5]
     fibroEset$species
     featureNames(fibroEset)[1:20]

