getLocalProbeIntensities   package:GeneRegionScan   R Documentation

_G_e_t _P_r_o_b_e _I_n_t_e_n_s_i_t_i_e_s _l_o_c_a_l_l_y

_D_e_s_c_r_i_p_t_i_o_n:

     Function that will create a ProbeLevelSet from cel files.

_U_s_a_g_e:

         getLocalProbeIntensities(listOfProbesets, celfilePath, annotation=NULL, aptCelExtractPath=NULL, pgfPath=NULL, clfPath=NULL,
         cdfPath=NULL, verbose=TRUE)

_A_r_g_u_m_e_n_t_s:

listOfProbesets: Either a character vector with the names of the
          probesets from which probes should be included in the
          ProbeLevelSet, or the path name of a file containing this

celfilePath: The path to a folder that contains the cel files of
          interest.

annotation: Character string specifying which type of arrays is
          investigated.

aptCelExtractPath: The path to the apt-cel-extract file from the
          Affymetrix Power Tools package (including the filename
          itself). You can try to leave it as NULL and see what
          happens. If the tool is in path, it will work anyway. If you
          have specified the argument before it will be remembered. If
          you are using an OS for which executables have been included
          in the package (win32 and linux64), it will use that.

 pgfPath: The path to a pgf file for the exon array of interest. This
          argument is mutually exclusive with the cdfPath argument.
          These files can be downloaded from www.affymetrix.com for the
          array of interest. Once given for a particular annotation,
          the location is saved for future use and can be given as NULL
          next time.

 clfPath: The path to a clf file for the exon array of interest. This
          argument is mutually exclusive with the cdfPath argument.
          These files can be downloaded from www.affymetrix.com for the
          array of interest. Once given for a particular annotation,
          the location is saved for future use and can be given as NULL
          next time.

 cdfPath: The path to a cdf file for the array of interest. This
          argument is mutually exclusive with the pgfPath and clfPath
          arguments. These files can be downloaded from
          www.affymetrix.com for the array of interest.  Once given for
          a particular annotation, the location is saved for future use
          and can be given as NULL next time.

 verbose: TRUE or FALSE.

_D_e_t_a_i_l_s:

     This is the workhorse function for generating ProbeLevelSets. It
     has two main functions: 1) It extracts the probe level intensity,
     normalizes it to all probes in the data using quantiles
     normalization and transfers  the results to the exprs part of a
     ProbeLevelSet. The extraction and normalization parts are done by
     a call to  the Affymetrix Power Tools (APT) function
     apt-cel-extract. The analysis switch for this call is '-a
     quant-norm,pm-only' and the documentation for APT can be used for
     further reference.  2) It extracts the probe sequences of all
     probes of interest. This is done using the [arrayname]probe
     packages for the 3'IVT type arrays for which they are available.
     For the exon type arrays, for which this is not available it is
     done by direct parsing of the pgf files using the readPgf function
     of the affxparser package. The results of this is saved in the
     featureData of the ProbeLevelSet

_V_a_l_u_e:

     A ProbeLevelSet with probe intensity values for all probes in the
     specified probesets. The ProbeLevelSet  inherits the
     ExpressionSet, but in addition it has the sequence of each probe
     stored in the featureData of the set.

_A_u_t_h_o_r(_s):

     Lasse Folkersen

_S_e_e _A_l_s_o:

     'getServerProbeIntensities', 'plotOnGene'

_E_x_a_m_p_l_e_s:

             ## Not run: 
             #must correct paths and give cel files before this example will work
             listOfProbesets<-c("10321_at")
             celfilePath<-path_to_some_cel_files
             aptCelExtractPath<-"~/apt/apt-cel-extract"
             cdfPath<-"~/hgu133plus2.cdf"
             getLocalProbeIntensities(listOfProbesets, celfilePath, annotation="hgu133plus2", aptCelExtractPath=aptCelExtractPath, cdfPath=cdfPath)
             
     ## End(Not run)

