ini.call                 package:xps                 R Documentation

_I_n_f_o_r_m_a_t_i_v_e/_N_o_n-_I_n_f_o_r_m_a_t_i_v_e _C_a_l_l

_D_e_s_c_r_i_p_t_i_o_n:

     Computes the Informative/Non-Informative Call for the exclusion of
     non-informative probe sets.

_U_s_a_g_e:

     ini.call(xps.data,
              filename   = character(0),
              filedir    = getwd(),
              tmpdir     = "",
              weight     = 0.5,
              mu         = 0.0,
              scale      = 1.0,
              tol        = 0.00001,
              cyc        = 100,
              alpha1     = 0.4,
              alpha2     = 0.6,
              version    = "1.3.1",
              option     = "transcript",
              exonlevel  = "",
              xps.scheme = NULL,
              add.data   = TRUE,
              verbose    = TRUE)

     xpsINICall(object, ...)

_A_r_g_u_m_e_n_t_s:

xps.data: object of class 'DataTreeSet'.

filename: file name of ROOT data file.

 filedir: system directory where ROOT data file should be stored.

  tmpdir: optional temporary directory where temporary ROOT files
          should be stored.

  weight: hyperparameter, usually set to 0.5 for 'version="1.3.1"' and
          to 8.0 for 'version="1.3.0"'.

      mu: hyperparameter allowing to correct for potential bias.

   scale: scaling parameter, usually set to 1.0 for 'version="1.3.1"'
          and to 2.0 for 'version="1.3.0"'.

     tol: termination tolerance for EM algorithm.

     cyc: maximum number of cycles of EM algorithm.

  alpha1: a significance threshold in (0,alpha2).

  alpha2: a significance threshold in (alpha1,1.0).

 version: version of original farms package. Currently,
          'version="1.3.1"' and 'version="1.3.0"' are implemented.
          Default is 'version="1.3.1"'.

  option: option determining the grouping of probes for summarization,
          one of  'transcript', 'exon', 'probeset'; exon arrays only.

exonlevel: exon annotation level determining which probes should be
          used for summarization; exon/genome arrays only.

xps.scheme: optional alternative 'SchemeTreeSet'.

add.data: logical. If 'TRUE' call data will be added to slots 'data'
          and 'detcall'.

 verbose: logical, if 'TRUE' print status information.

  object: object of class 'DataTreeSet'.

     ...: the arguments described above.

_D_e_t_a_i_l_s:

     In contrast to 'mas5.call' this function quantifies the
     signal-to-noise ratio for each probe set, as described in Talloen
     et al. Thus, the returned p-values and detection calls have a
     different meaning:

     The p-value that is returned estimates the signal-to-noise ratio
     (SNR): 
      P-values (SNR) of less than 0.5 indicate that there is more
     signal than noise and the corresponding genes are considered to be
     'informative' for further analysis. In contrast, values greater
     than 0.5 indicate 'non-informative' genes.

     The informative call is computed by thresholding the p-value as
     in:

     call "P" if p-value < alpha1 
      call "M" if alpha1 <= p-value < alpha2 
      call "A" if alpha2 <= p-value

     Here "P" should be considered as informative "I", "M" as
     marginally informative, and "A" as non-informative "NI".

     The defaults for 'alpha1=0.4' and 'alpha2=0.6' are set to allow
     "M" calls. In order to get the same results as package
     'farms_1.3.1', you need to set 'alpha1=0.5' and 'alpha2=0.5'.

     For exon/genome arrays it is necessary to supply 'option' and
     'exonlevel'.

     Following 'option's are valid for exon arrays only:

       'transcript':  expression levels are computed for transcript clusters, i.e. probe sets containing the same 'transcript_cluster_id'.
       'exon':        expression levels are computed for exon clusters, i.e. probe sets containing the same 'exon_id', where each exon cluster consists of one or more 'probeset's.
       'probeset':    expression levels are computed for individual probe sets, i.e. for each 'probeset_id'.

     Following 'exonlevel' annotations are valid for exon arrays:

         'core':          probesets supported by RefSeq and full-length GenBank transcripts.
         'metacore':      core meta-probesets.
         'extended':      probesets with other cDNA support.
         'metaextended':  extended meta-probesets.
         'full':          probesets supported by gene predictions only.
         'metafull':      full meta-probesets.
         'ambiguous':     ambiguous probesets only.
         'affx':          standard AFFX controls.
         'all':           combination of above.

     Following 'exonlevel' annotations are valid for whole genome
     arrays:

         'core':      probesets with category 'unique' and 'mixed'.
         'metacore':  probesets with category 'unique' only.
         'affx':      standard AFFX controls.
         'all':       combination of above.

     Exon levels can also be combined, with following combinations
     being most useful:

       'exonlevel="metacore+affy"':       core meta-probesets plus AFFX controls
       'exonlevel="core+extended"':       probesets with cDNA support
       'exonlevel="core+extended+full"':  supported plus predicted probesets

     Exon level annotations are described in the Affymetrix whitepaper
     'exon_probeset_trans_clust_whitepaper.pdf'.

     In order to use an alternative 'SchemeTreeSet' set the
     corresponding SchemeTreeSet 'xps.scheme'.

     'xpsINICall' is the 'DataTreeSet' method called by function
     'ini.call',  containing the same parameters.

_V_a_l_u_e:

     A 'CallTreeSet'

_N_o_t_e:

     Since I/NI-calls distinguish only between informative and
     non-informative genes, the calls are identical for all samples.

_A_u_t_h_o_r(_s):

     Christian Stratowa

_R_e_f_e_r_e_n_c_e_s:

     Talloen, W., Clevert D.-A., Hochreiter, S., Amaratunga, D.,
     Bijnens, J., Kass, S., and Gohlmann, H.W.H. (2006), I/NI-calls for
     the exclusion of non-informative genes: a highly effective
     filtering tool for microarray data. Bioinformatics
     23(21):2897-2902

_S_e_e _A_l_s_o:

     'farms', 'mas5.call'

_E_x_a_m_p_l_e_s:

     ## first, load ROOT scheme file and ROOT data file
     scheme.test3 <- root.scheme(paste(.path.package("xps"),"schemes/SchemeTest3.root",sep="/"))
     data.test3 <- root.data(scheme.test3, paste(.path.package("xps"),"rootdata/DataTest3_cel.root",sep="/"))

     ## I/NI call
     call.ini <- ini.call(data.test3,"tmp_Test3INI",verbose=FALSE)

     ## get data.frames
     snr.ini <- pvalData(call.ini)
     inf.ini <- presCall(call.ini)
     head(snr.ini)
     head(inf.ini)

     ## plot results
     if (interactive()) {
     callplot(call.ini)
     }

     rm(scheme.test3, data.test3)
     gc()

