get.annotation          package:simpleaffy          R Documentation

_G_e_t _a_n_n_o_t_a_t_i_o_n _d_a_t_a _f_o_r _a _g_e_n_e _l_i_s_t

_D_e_s_c_r_i_p_t_i_o_n:

     Takes a vector of probeset names and a CDF name. Produces a table
     of annotations, containing gene name, description, sequence
     accession number and unigene accession number for each probeset.
     In addition, write.annotation is a utility function that outputs
     the annotation data in a form suitable for loading into excel and
     results.summary takes the outut of pairwise.comparison or
     pairwise.filter and spits out a table with the means of the
     replicates the fold-change between them (log2) and t-test
     p-values. This is followed by a table of annotation (produced by
     get.annotation).

_U_s_a_g_e:

     get.annotation(x, cdfname,verbose=FALSE)
     write.annotation(summary,file="results/annotation.table.xls")
     results.summary(results,cdfname)

_A_r_g_u_m_e_n_t_s:

       x: a vector of probe names 

 cdfname: the name of the chip (as produced by cdfName(AffyBatch) 

 verbose: print out information if problems are found looking things up
          in the annotation data 

 summary: a table of data to write in a format appropriate to read into
          Excel 

    file: a table delimited file 

 results: a PairComp object, as produced by pairwise.comparison and
          pairwise.filter 

_V_a_l_u_e:

     A table containing annotation data

_A_u_t_h_o_r(_s):

     Crispin J Miller

_R_e_f_e_r_e_n_c_e_s:

     http://bioinformatics.picr.man.ac.uk/

_E_x_a_m_p_l_e_s:

      ## Not run: 
        pw       <- pairwise.comparison(eset.rma,"group",c("A","P"))
        pw.filtered <- pairwise.filter(pw)
        summary     <- results.summary(pw.filtered,"hgu133a")
        write.annotation(file="spreadsheet.xls",summary)
       
     ## End(Not run)