result2html           package:AffyExpress           R Documentation

_o_u_t_p_u_t _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 _t_o _a _H_T_M_L _f_i_l_e

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

     output differentially expressed genes to a HTML file based on a
     result table from the select.sig.gene function.  It contais the 
     following columns:  Probe, Symbol, Description, GenBank,
     LocusLink, Log2ratio, and p value.

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

     result2html(cdf.name, result, filename="result")

_A_r_g_u_m_e_n_t_s:

cdf.name: cdf name which can be obtained from the annotation function

  result: a data frame returned from the gene.select function

filename: a file name for the output

_A_u_t_h_o_r(_s):

     Xiwei Wu xwu@coh.org, Xuejun Arthur Li xueli@coh.org

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

     data(testData)
     normaldata<-pre.process("rma",testData)
     ## Create design matrix
     design<-make.design(pData(normaldata), "group")

     ## Create contrast matrix - Compare group "A" vs. "C"
     contrast<-make.contrast(design, "A", "C")

     ## Identify differentially expressed gene by using LIMMA method
     result<-regress(normaldata, design, contrast, "L")

     ## Select differentially expressed gene based on p <0.05 and 
     ## fold change >=log2(1.5)
     select<-select.sig.gene(result, p.value=0.05, m.value=log2(1.5))

     ## Output differentially expressed gene to a example.html
     result2html(annotation(normaldata), select, "example")

