justRMA                 package:affy                 R Documentation

_R_e_a_d _C_E_L _f_i_l_e_s _i_n_t_o _a_n _E_x_p_r_e_s_s_i_o_n_S_e_t

_D_e_s_c_r_i_p_t_i_o_n:

     Read CEL files and compute an expression measure without using an
     AffyBatch.

_U_s_a_g_e:

     just.rma(..., 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, background=TRUE, normalize=TRUE,
                    bgversion=2, destructive=FALSE, cdfname = NULL)

     justRMA(..., 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,
                   hdf5=FALSE, hdf5FilePath=NULL,verbose=FALSE,
                   normalize=TRUE, background=TRUE, 
                   bgversion=2, destructive=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 'AnnotatedDataFrame' 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', then overrides what is in 'rm.mask' and
          'rm.oultiers'.

    hdf5: use of hdf5 ? (not available yet)

hdf5FilePath: a filename to use with hdf5 (not available yet).

 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'.

normalize: logical value. If 'TRUE', then normalize data using quantile
          normalization.

background: logical value. If 'TRUE', then background correct using RMA
          background correction.

bgversion: integer value indicating which RMA background to use 1: use
          background similar to pure R rma background given in affy
          version 1.0 - 1.0.2 2: use background similar to pure R rma
          background given in affy version 1.1 and above

destructive: logical value. If 'TRUE', then works on the PM matrix in
          place as much as possible, good for large datasets.

 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:

     'justRMA' is a wrapper for 'just.rma' 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 'justRMA()', then all
     the CEL files in the working directory are read, converted to an
     expression measure using RMA and put into an 'ExpressionSet'.
     However, the arguments give the user great flexibility.

     'phenoData' is read using 'read.AnnotatedDataFrame'. If a
     character is given, it tries to read the file with that name to
     obtain the 'AnnotatedDataFrame' object as described in
     'read.AnnotatedDataFrame'. If left 'NULL' and 'widget=FALSE'
     ('widget=TRUE' is not currently supported), then a default object
     is created. It will be an object of class 'AnnotatedDataFrame'
     with its pData being a data.frame with column x indexing the CEL
     files.

     '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..

     The arguments 'rm.masks', 'rm.outliers', 'rm.extra' are passed
     along to the function 'read.celfile'.

_V_a_l_u_e:

     An 'ExpressionSet' object, containing expression values identical
     to what one would get from running 'rma' on an 'AffyBatch'.

_A_u_t_h_o_r(_s):

     In the beginning: James MacDonald <jmacdon@med.umich.edu>
     Supporting routines, maintenance and just.rma: Ben Bolstad
     <bmb@bmbolstad.com>

_S_e_e _A_l_s_o:

     'rma','ReadAffy'

