read.affy.mixed          package:simpleaffy          R Documentation

_R_e_a_d _a _S_e_t _o_f ._C_E_L _F_i_l_e_s _a_n_d _P_h_e_n_o_t_y_p_i_c _D_a_t_a _f_r_o_m _m_i_x_e_d _c_h_i_p _t_y_p_e_s

_D_e_s_c_r_i_p_t_i_o_n:

     Reads the specified file, which defines phenotypic data for a set
     of .CEL files. Reads the specified files into an 'AffyBatch'
     object and then creates a 'phenoData' object, defining the
     experimental factors  for those chips. This function deals with
     different array types by generating a pseudo arrayset containing
     only the probes in common. It does this by finding the smallest
     chip type in the set, and using this as a template. Probesets that
     aren't shared are set to 0. Other probesets are copied in. Note
     that this means that spots that were in one place on one array,
     appear to be at a different place on another. What this does to
     position specific background correction algorithms (such as mas5)
     is left as an exercise to the reader). Beware...

_U_s_a_g_e:

     read.affy.mixed(covdesc = "covdesc",path=".", ...)

_A_r_g_u_m_e_n_t_s:

 covdesc: A white space delimited file suitable for reading as a
          'data.frame'. The first column (with no column name)  
          contains the names(or paths to) the .CEL files to read.
          Remaining columns (with names) represent experimental factors
          for each chip. these become elements of the 'phenoData'
          object. 

     ...: extra functions to pass on to 'ReadAffy' 

    path: The path to prefix the filenames with before calling
          'ReadAffy' 

_D_e_t_a_i_l_s:

_V_a_l_u_e:

     An AffyBatch object

_A_u_t_h_o_r(_s):

     Crispin J Miller

_R_e_f_e_r_e_n_c_e_s:

     <URL:  http://bioinformatics.picr.man.ac.uk/>

_S_e_e _A_l_s_o:

     'ReadAffy', 'AffyBatch' 'data.frame' 'phenoData'

_E_x_a_m_p_l_e_s:

      
       ## Not run: 
         eset <- read.affy.mixed(); # read a set of CEL files
       
         eset.rma <- call.exprs(eset,"rma");   
       
     ## End(Not run)