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,sd=FALSE, cdfname = NULL)

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

_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'

      sd: should the standard deviation values in the CEL file be read
          in. Since these are typically not used default is not to read
          them in. This also save lots of memory.

 cdfname: Used to specify the name of an alternative cdf package. If
          set to 'NULL', the usual cdf package based on Affymetrix'
          mappings will be used.

_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 called 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 'read.phenoData'. If a character is
     given it tries to read the file with that name to obtain the
     phenoData object as described in '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"))'

     'AllButCelsForReadAffy' is an internal function that gets called
     by 'ReadAffy'. It gets all the information except the cel
     intensities.

     'description' is read using 'read.MIAME'. If a character is given
     it tries to read the file with that name to obtain a 'MIAME'
     instance. If left 'NULL' but 'widget=TRUE' then widgets are used.
     If left 'NULL' and 'widget=FALSE' then an empty instance of
     'MIAME' is created..

_V_a_l_u_e:

     An 'AffyBatch' object.

_A_u_t_h_o_r(_s):

     Ben Bolstad bmb@bmbolstad.com (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)
     }

