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("AnnotatedDataFrame"),
                    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: an 'AnnotatedDataFrame' object, a 'character' of length one,
          or a 'data.frame'.

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', then 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', then 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.

     If 'phenoData' is a character vector of length 1, the function
     'read.AnnotatedDataFrame' is called to read a file of that name
     and produce the 'AnnotationDataFrame' object with the sample
     metadata. If 'phenoData' is a 'data.frame', it is converted to an
     'AnnotatedDataFrame'. If it is 'NULL' and 'widget=FALSE'
     ('widget=TRUE' is not currently supported), then a default object
     of class 'AnnotatedDataFrame' is created, whose 'pData' is a
     data.frame with rownames being the names of the CEL files, and
     with one column 'sample' with an integer index.

     '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,
     then 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 <- system.file("celfiles", package="affydata")
          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)
     }

