aggregateExprs             package:PGSEA             R Documentation

_A_g_g_r_e_g_a_t_e _e_x_p_r_e_s_s_i_o_n _d_a_t_a

_D_e_s_c_r_i_p_t_i_o_n:

     This function removes duplicates row names from an expression set,
     summarizing them with a function of the users choice. The "absMax"
     function located in package "reb" we have found to be useful.

_U_s_a_g_e:

     aggregateExprs(x, package = "hgu133plus2", using = "ENTREZID", FUN, ...)

_A_r_g_u_m_e_n_t_s:

       x: expression data - matrix, eSet, or ExpressionSet 

 package: annotation package of expression data 

   using: format type that gene IDs are converted to  

     FUN: function by which to summarize duplicated values 

     ...: extra parameters passed on to FUN 

_V_a_l_u_e:

     A matrix of expression data with the rows aggregated to a unique
     format chosen by the user. The new identifiers of the returned
     matrix are those specified with the "using" argument. To see
     possible values, use the ls() command illustrated below in the
     examples.

_A_u_t_h_o_r(_s):

     Kyle Furge <kyle.furge@vai.org> and Karl Dykema
     <karl.dykema@vai.org>

_E_x_a_m_p_l_e_s:

             if (require(hgu95av2.db) & require(annaffy)) {
                     library(annaffy)
                     data(aafExpr)
                     class(exprs(aafExpr))
                     exprs(aafExpr)[1:4, 1:4]

                     #list possible values for the "using" argument
                     ls(pos=which(search()=="package:hgu95av2.db"))

                     convert <- aggregateExprs(exprs(aafExpr),"hgu95av2.db",FUN=mean,na.rm=TRUE)
                     convert[1:4,1:4]
             }

