GSint               package:GeneSpring               R Documentation

_C_r_e_a_t_i_o_n _o_f _G_S_i_n_t _c_l_a_s_s _o_b_j_e_c_t

_D_e_s_c_r_i_p_t_i_o_n:

     The 'GSint' class object contains the expression values and the
     annotations of the GeneSpring Expriment Interpretation object.
     Apart from the 'new' function, the function 'GSint' can be used to
     create a new 'GSint' object.

_U_s_a_g_e:

     GSint(expName = "GeneSpring experiment",
             a.nor = matrix(nc = 0, nr = 0),
             se.nor = matrix(nc = 0, nr = 0),
             sd.nor = matrix(nc = 0, nr = 0),
             n.nor = matrix(nc = 0, nr = 0),
             a.raw = matrix(nc = 0, nr = 0), 
             se.raw = matrix(nc = 0, nr = 0), 
             sd.raw = matrix(nc = 0, nr = 0), 
             n.raw = matrix(nc = 0, nr = 0),
             a.ctr = matrix(nc = 0, nr = 0),
             se.ctr = matrix(nc = 0, nr = 0),
             sd.ctr = matrix(nc = 0, nr = 0),
             n.ctr = matrix(nc = 0, nr = 0),
             expparam = data.frame(),
             numConditions = 0,
             ngenes = 0,
             genenames = c("")
     )

_A_r_g_u_m_e_n_t_s:

 expName: Experiment name

   a.nor: Matrix representing the AVERAGE expression values for the
          NORMALIZED expression values

  se.nor: Matrix representing the STANDARD ERROR for the NORMALIZED
          expression values

  sd.nor: Matrix representing the STANDARD DEVIATION for the NORMALIZED
          expression values

   n.nor: Matrix representing the NUMBER OF REPLICATES in this
          condition for the NORMALIZED values

   a.raw: Matrix representing the AVERAGE expression values for the RAW
          expression values

  se.raw: Matrix representing the STANDARD ERROR for the RAW expression
          values

  sd.raw: Matrix representing the STANDARD DEVIATION for the RAW
          expression values

   n.raw: Matrix representing the NUMBER OF REPLICATES in this
          condition for the RAW values

   a.ctr: Matrix representing the AVERAGE expression values for the
          CONTROL values

  se.ctr: Matrix representing the STANDARD ERROR for the CONTROL values

  sd.ctr: Matrix representing the STANDARD DEVIATION for the CONTROL
          values

   n.ctr: Matrix representing the NUMBER OF REPLICATES in this
          condition for the CONTROL values

expparam: Data drame representin the sample attributes or experimental
          parameters

numConditions: Numeric value representing the number of conditions (or
          samples) in this interpretaion or experiment

  ngenes: Numeric values representing the number of genes in the
          experiment

genenames: List representing the gene names in the experiment

_D_e_t_a_i_l_s:

     The 'GSint' class object is a representation of a GeneSpring
     Experiment Interpretation. The object consists of 17 slots:

     1) The name of the experiment (slot: expName) 2) Twelve slots
     representing the various types of expression data as matrix
     objects 3) The experimental parameters (slot: expparam) 4) The
     number of samples or conditions in the experiment (slot:
     numConditions) 5) The number of genes (slot: ngenes) 5) A list of
     the gene names(slot: genenames)

     All of the expression value slots are optional and are not
     guaranteed to contain data. When a GeneSpring Experiment is read
     in from file, only the a.nor slot and optionally the a.ctr slot
     will contain data. When a GeneSpring Experiment INTERPRETATION is
     read, any of the 12 expression values slots could contain data.
     Which data slots are filled is dependent on which choices were
     made in the construction of the external programs in GeneSpring.

     For more information about GeneSpring external programs see the
     GeneSpring manual. For more information about the differences
     between an Experiment and an Interpretation see the R manual
     entries for 'GSload.int' and 'GSload.exp'.

_V_a_l_u_e:

     Both 'GSint' and 'new' return an object of class 'GSint'.

_M_e_t_h_o_d_s:

     _s_h_o_w 'signature(object = "GSint")': Produces a short description
          of the GSint class. It lists all the objects contained in the
          class. 

_N_o_t_e:

     This and any other functions in the GeneSpring package are only
     useful, when using Agilent Technologies Gene Expression software
     GeneSpring.

_A_u_t_h_o_r(_s):

     Thon de Boer, Agilent Technologies, Santa Clara, CA, USA
     thon_deboer@agilent.com

_R_e_f_e_r_e_n_c_e_s:

     For more information on using GeneSpring with R see <URL:
     http://www.chem.agilent.com/scripts/generic.asp?lpage=34733>

_S_e_e _A_l_s_o:

     'GSload.int', 'GSload.exp', 'GSsave.exp', 'GSint2BC', 'BC2GSint'

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

     #Create some simple sample annotation
     ep <- t(data.frame(SampleName=1:10))
     #Create a GSint object with random data as the RAW data object
     gs.int <- GSint(expName="Random data",a.raw=matrix(rnorm(1000),nc=10),expparam=ep, genenames=1:100)

     gs.int@expName
     t(gs.int@expparam)

