dyebias.geo2marray      package:dyebiasexamples      R Documentation

_c_o_n_v_e_n_i_e_n_c_e _f_u_n_c_t_i_o_n _t_o _c_o_n_v_e_r_t _G_E_O _o_b_j_e_c_t_s _t_o _m_a_r_r_a_y _o_b_j_e_c_t_s

_D_e_s_c_r_i_p_t_i_o_n:

     convenience function to convert GEO objects to marray objects

_A_r_g_u_m_e_n_t_s:

     gse: GSE data set 

slide.ids: Return only the slides with these ids. If NULL, return all.

    type: what to extract; must be either "norm" or "raw". 

gene.selector: function(table) acting on Table(GPL) giving back  an
          index with the rows considered to be genes. 

reporterid.name: column containing the reporter.id, in Table(gpl).

cy3.name: The column name containing the factor value for the Cy3
          (green) channel 

cy5.name: The column name containing the factor value for the Cy5 (red)
          channel 

  R.name: column name for extracting the R data from Table(gsm) 

  G.name: column name for extracting the G data from Table(gsm) 

  M.name: column name for extracting the M data from Table(gsm) 

  A.name: column name for extracting the A data from Table(gsm) 

 Rf.name: column name for extracting the Rf data from Table(gsm) 

 Gf.name: column name for extracting the Gf data from Table(gsm) 

 Rb.name: column name for extracting the Rb data from Table(gsm) 

 Gb.name: column name for extracting the Gb data from Table(gsm) 

_D_e_t_a_i_l_s:

     The 'XYZ.name' mechanism is the same as that used in 
     'read.marrayRaw'; i.e. you specify the name of the column that
     contains the desired data.

_V_a_l_u_e:

     A full-fledged  marrayRaw (if 'type' was "raw") or marrayNorm (if
     'type' was "norm") is returned.

_N_o_t_e:

     At some point, this functionality should be merged into the
     convert package.

_A_u_t_h_o_r(_s):

     Philip Lijnzaad

_R_e_f_e_r_e_n_c_e_s:

     Davis, S. and Meltzer, P.S (2007). GEOquery: a bridge between the
     Gene Expression Omnibus (GEO) and BioConductor. _Bioinformatics_
     23, 1846-1847 (doi:10.1093/bioinformatics/btm254).

     Dudoit, S. and Yang, Y.H. (2002)  Bioconductor R packages for
     exploratory analysis and normalization of cDNA microarray data.
     In: Parmigiani, G., Garrett, E.S. , Irizarry, R.A., and Zeger,
     S.L. (eds.) _The Analysis of Gene Expression Data: Methods and
     Software_, New~York: Springer

     Chen,S., de~Vries, M.A. and Bell, S.P. (2007) _Genes Dev._ 21,
     2897-2907 "Orc6 is required for dynamic recruitment of Cdt1 during
     repeated Mcm2-7 loading" (doi:10.1101/gad.1596807)

_E_x_a_m_p_l_e_s:

                                            

     ## Not run: 
       ## Running this example takes too much time; if you want that, see the
       ## second example in the vignette
     ## End(Not run)                                       

