Converting             package:GEOquery             R Documentation

_C_o_n_v_e_r_t _a _G_D_S _d_a_t_a_s_t_r_u_c_t_u_r_e _t_o _a _B_i_o_C_o_n_d_u_c_t_o_r _d_a_t_a_s_t_r_u_c_t_u_r_e

_D_e_s_c_r_i_p_t_i_o_n:

     Functions to take a GDS data structure from getGEO and coerce it
     to limma MALists or exprSets.

_U_s_a_g_e:

     GDS2MA(GDS,do.log2=FALSE,GPL=NULL)
     GDS2eSet(GDS,do.log2=FALSE)

_A_r_g_u_m_e_n_t_s:

     GDS: The GDS datastructure returned by getGEO

 do.log2: Boolean, should the data in the GDS be log2 transformed
          before inserting into the new data structure

     GPL: Either a GPL data structure (from a call to getGEO) or NULL. 
          If NULL, this will cause a call to getGEO to produce a GPL.
          The gene information from the GPL is then used to construct
          the 'genes' slot of the resulting limma 'MAList' object.

_D_e_t_a_i_l_s:

     This function just rearranges one data structure into another. 
     For GDS, it also deals appropriately with making the "targets"
     list item for the limma data structure and the phenoData slot of
     exprSets.

_V_a_l_u_e:

  GDS2MA: A limma MAList

GDS2eSet: A exprSet object

_A_u_t_h_o_r(_s):

     Sean Davis

_R_e_f_e_r_e_n_c_e_s:

     See the limma and exprSet help in the appropriate packages

_E_x_a_m_p_l_e_s:

     ## Not run: gds505 <- getGEO('GDS505')
     ## Not run: MA <- GDS2MA(gds505)
     ## Not run: eset <- GDS2eSet(gds505)