getServerProbeIntensities   package:GeneRegionScan   R Documentation

_G_e_t _P_r_o_b_e _I_n_t_e_n_s_i_t_i_e_s _f_r_o_m _a _s_e_r_v_e_r

_D_e_s_c_r_i_p_t_i_o_n:

     Wrapper around getLocalProbeIntensities that is designed to be run
     easily on remote computers.

_U_s_a_g_e:

         getServerProbeIntensities(listOfProbesets, celfilePath, annotation=NULL, aptCelExtractPath=NULL, pgfPath=NULL, clfPath=NULL, cdfPath=NULL, serveradress="localhost", username=NULL, password=NULL, plinkPath=NULL, pscpPath=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. If serveradress is different from "localhost", this
          should be the path on the remote computer

annotation: Character string specifying which type of arrays is
          investigated. If a pgf file and clf file is specified this is
          optional.

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 default to using
          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.

serveradress: Character string with the IP adress to a remote server.
          Defaults to "localhost", in which case the algorithm is run
          locally.

username: The username for the remote server. Optional if serveradress
          is "localhost".

password: The password for the remote server. Optional if serveradress
          is "localhost".

plinkPath: The path to the plink program. Can be found at
          http://www.chiark.greenend.org.uk/~sgtatham/putty/download.html.
          Used to transfer commands to the remote server. Optional if
          serveradress is "localhost".

pscpPath: The path to the pscp program. Can be found at
          http://www.chiark.greenend.org.uk/~sgtatham/putty/download.html.
          Used to transfer commands to the remote server. Optional if
          serveradress is "localhost".

 verbose: TRUE or FALSE.

_D_e_t_a_i_l_s:

     This function is a wrapper around getLocalProbeIntensities. The
     main function of the getServerProbeIntensities  function is to
     save all the data needed to start a getLocalProbeIntensities run,
     send it to a remote server, start the run, and return the data.
     This is useful if you have access to a fast server and want to
     work with large datasets of exon arrays.

_V_a_l_u_e:

     A ProbeLevelSet with probe quantiles normalized 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:

     'getLocalProbeIntensities', 'plotOnGene'

_E_x_a_m_p_l_e_s:

             ## Not run: 
             #must correct paths, username and password before this example will work
             listOfProbesets<-c("10321_at")
             celfilePath<-path_to_some_cel_files #remote
             aptCelExtractPath<-"~/apt/apt-cel-extract" #remote
             cdfPath<-"~/hgu133plus2.cdf" #remote
             username<-"user1"
             password<-"ZaphodBeeblebrox"
             plinkPath<-"~/plink" #local
             pscpPath<-"~/pscp" #local
             getServerProbeIntensities(listOfProbesets, celfilePath, annotation="hgu133plus2", aptCelExtractPath=aptCelExtractPath, cdfPath=cdfPath,
             username=username, password=password, plinkPath=plinkPath, pscpPath=pscpPath)

             ## End(Not run)

