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 ExpressionSets.

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

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

_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 or
          the 'featureData' slot of the 'ExpressionSet' instance. 

AnnotGPL: In general, the annotation GPL files will be available for
          GDS records, so the default is to use these files over the
          user-submitted GPL files

_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
     ExpressionSets.

_V_a_l_u_e:

  GDS2MA: A limma MAList

GDS2eSet: An ExpressionSet object

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

     Sean Davis

_R_e_f_e_r_e_n_c_e_s:

     See the limma and ExpressionSet 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)

