justRMA                 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 and compute an expression measure using affybatch.

_U_s_a_g_e:

     just.rma(..., 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, 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 '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' 

    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 call 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.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 an
     object of class 'phenoData' with
     'new("phenoData",pData=data.frame(x=1:length(CELfiles)),varLabels=
     list(x="arbitrary number"))'

     '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.

_A_u_t_h_o_r(_s):

     In the beginning: James MacDonald <jmacdon@med.umich.edu>
     Supporting routines, maintainence 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:

