read.affybatch             package:affy             R Documentation

_R_e_a_d _C_E_L _f_i_l_e_s _i_n_t_o _a_n _A_f_f_y_B_a_t_c_h

_D_e_s_c_r_i_p_t_i_o_n:

     Read CEL files into an Affybatch

_U_s_a_g_e:

     read.affybatch(..., filenames = character(0),
                    phenoData = new("phenoData"),
                    description = NULL,
                    notes = "",
                    compress = getOption("BioC")$affy$compress.cel,
                    rm.mask = FALSE, rm.outliers = FALSE, rm.extra = FALSE,
                    verbose = FALSE)

     ReadAffy(..., filenames=character(0),
                   widget=getOption("BioC")$affy$use.widgets,
                   compress=getOption("BioC")$affy$compress.cel,
                   celfile.path=getwd(),
                   sampleNames=NULL,
                   phenoData=NULL,
                   description=NULL,
                   notes="",
                   rm.mask=FALSE, rm.outliers=FALSE, rm.extra=FALSE,
                   verbose=FALSE)

_A_r_g_u_m_e_n_t_s:

     ...: file names separated by comma.

filenames: file names in a character vector.

phenoData: a 'phenoData' object

description: a 'MIAME' object 

   notes: notes 

compress: are the CEL files compressed ?

 rm.mask: should the spots marked as 'MASKS' set to 'NA' ? 

rm.outliers: should the spots marked as 'OUTLIERS' set to 'NA' 

rm.extra: if 'TRUE', overrides what is in 'rm.mask' and 'rm.oultiers' 

 verbose: verbosity flag 

  widget: a logical specifying if widgets should be used.

celfile.path: a character denoting the path 'ReadAffy' should look for
          cel files

sampleNames: a character vector of sample names to be used in the
          'AffyBatch'

_D_e_t_a_i_l_s:

     'ReadAffy' is a wrapper for 'read.affybatch' that permits the user
     to read in phenoData, MIAME information, and CEL files using
     widgets. One can also define files where to read phenoData and
     MIAME information.

     If the function is call with no arguments 'ReadAffy()' all the CEL
     files in the working directory are read and put into an
     'AffyBatch'. However, the arguments give the user great
     flexibility.

     'phenoData' is read using 'link[Biobase]{read.phenoData}'. If a
     character is given it tries to read the file with that name to
     obtain the phenoData object as described in
     'link[Biobase]{read.phenoData}'. If left 'NULL' but 'widget=TRUE'
     then widgets are used. If left 'NULL' and 'widget=FALSE' then a
     default object is created. It will be a data frame with
     'new("phenoData",pData=data.frame(x=1:length(CELfiles)),varLabels=
     list(x="arbitrary number"))'

_V_a_l_u_e:

     An 'AffyBatch' object.

_A_u_t_h_o_r(_s):

     Ben Bolstad bolstad@stat.berkeley.edu (read.affybatch), Laurent
     Gautier, and Rafael A. Irizarry (ReadAffy)

_S_e_e _A_l_s_o:

     'AffyBatch'

_E_x_a_m_p_l_e_s:

     if(require(affydata)){
          celpath <- paste(.path.package("affydata"),"celfiles",sep="/")
          fns <- list.celfiles(path=celpath,full.names=TRUE)
      
          cat("Reading files:\n",paste(fns,collapse="\n"),"\n")
          ##read a binary celfile
          abatch <- ReadAffy(filenames=fns[1])
          ##read a text celfile
          abatch <- ReadAffy(filenames=fns[2])
          ##read all files in that dir
          abatch <- ReadAffy(celfile.path=celpath)
     }

