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_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', 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' normalize data using quantile
          normalization

background: logical value. If 'TRUE' 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' 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', 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 'exprSet'. 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 phenoData 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 pData 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 'exprSet' 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'

_E_x_a_m_p_l_e_s:

