AffyBatch-class             package:affy             R Documentation

_C_l_a_s_s _A_f_f_y_B_a_t_c_h

_D_e_s_c_r_i_p_t_i_o_n:

     This is a class representation for Affymetrix GeneChip probe level
     data. The main component are the intensities from multiple arrays
     of the same 'CDF' type. It extends 'eSet'.

_O_b_j_e_c_t_s _f_r_o_m _t_h_e _C_l_a_s_s:

     Objects can be created using the function 'read.affybatch' or the
     wrapper 'ReadAffy'.

_S_l_o_t_s:


     '_c_d_f_N_a_m_e': Object of class 'character' representing the name of
          'CDF' file associated with the arrays in the 'AffyBatch'.

     '_n_r_o_w': Object of class 'integer' representing the physical number
          of rows in the arrays.

     '_n_c_o_l': Object of class 'integer' representing the physical number
          of columns in the arrays.

     '_a_s_s_a_y_D_a_t_a': Object of class 'AssayData' containing the raw data,
          which will be at minimum a matrix of intensity values. This
          slot can also hold a matrix of standard errors if the 'sd'
          argument is set to 'TRUE' in the call to 'ReadAffy'. 

     '_p_h_e_n_o_D_a_t_a': Object of class 'AnnotatedDataFrame' containing
          phenotypic data for the samples.

     '_a_n_n_o_t_a_t_i_o_n' A character string identifying the annotation that
          may be used for the 'ExpressionSet' instance.

     '_f_e_a_t_u_r_e_D_a_t_a' Object of class 'AnnotatedDataFrame' containing
          feature-level (e.g., probeset-level) information.

     '_e_x_p_e_r_i_m_e_n_t_D_a_t_a': Object of class "MIAME" containing
          experiment-level information. 

     '_n_o_t_e_s': Object of class "character" Vector of explanatory text 

_E_x_t_e_n_d_s:

     Class '"eSet"', directly.

_M_e_t_h_o_d_s:


     _c_d_f_N_a_m_e 'signature(object = "AffyBatch")': Obtains the cdfName
          slot.

     _p_m<- 'signature(object = "AffyBatch")': replaces the perfect match
          intensities 

     _p_m 'signature(object = "AffyBatch")': extracts the pm intensities. 

     _m_m<- 'signature(object = "AffyBatch")': replaces the mismatch
          intensities.

     _m_m 'signature(object = "AffyBatch")': extracts the mm intensities. 

     _p_r_o_b_e_s 'signature(object = "AffyBatch", which)': extract the
          perfect match or mismatch probe intensities. Uses which can
          be "pm" and "mm".

     _e_x_p_r_s 'signature(object = "AffyBatch")': extracts the expression
          matrix.

     _e_x_p_r_s<- 'signature(object = "AffyBatch", value = "matrix")':
          replaces the expression matrix.

     _s_e._e_x_p_r_s 'signature(object = "AffyBatch")': extracts the matrix of
          standard errors of expression values, if available.

     _s_e._e_x_p_r_s<- 'signature(object = "AffyBatch", value = "matrix")':
          replaces the matrix of standard errors of expression values.

     [<- 'signature(x = "AffyBatch")': replaces subsets. 

     [ 'signature(x = "AffyBatch")': subsets by array.

     _b_o_x_p_l_o_t 'signature(x = "AffyBatch")':  creates a 'boxplots of log
          base 2 intensities (pm, mm or both). Defaults to both.'

     _h_i_s_t 'signature(x = "AffyBatch")':  creates a plot showing all the
          histograms of the pm,mm or both data. See 'plotDensity'

     _c_o_m_p_u_t_e_E_x_p_r_S_e_t 'signature(x = "AffyBatch", summary.method =
          "character")': For each probe set computes an expression
          value using 'summary.method'. 

     _f_e_a_t_u_r_e_N_a_m_e_s 'signature(object = "AffyBatch")': return the probe
          set names also referred to as the Affymetrix IDs. Notice that
          one can not assign 'featureNames'. You must do this by
          changing the cdfenvs.

     _g_e_n_e_N_a_m_e_s 'signature(object="AffyBatch'")': deprecated, use
          'featureNames'

     _g_e_t_C_d_f_I_n_f_o 'signature(object = "AffyBatch")': retrieve the
          environment that defines the location of probes by probe set. 

     _i_m_a_g_e 'signature(x = "AffyBatch")': creates an image for each
          sample.

     _i_n_d_e_x_P_r_o_b_e_s 'signature(object = "AffyBatch", which =
          "character")': returns a  list with locations of the probes
          in each probe set. The affyID corresponding to the probe set
          to retrieve can be specified in an optional parameter
          'genenames'. By default, all the affyIDs are retrieved. The
          names of the elements in the list returned are the affyIDs.
          'which' can be "pm", "mm", or "both". If "both" then perfect
          match locations are given followed by mismatch locations.

          'signature(object = "AffyBatch", which = "missing")' (i.e.,
          calling 'indexProbes' without a "which" argument) is the same
          as setting "which" to "pm". 

     _i_n_t_e_n_s_i_t_y<- 'signature(object = "AffyBatch")': a replacement
          method for the 'exprs' slot, i.e. the intensities. 

     _i_n_t_e_n_s_i_t_y 'signature(object = "AffyBatch")': extract the 'exprs'
          slot, i.e. the intensities. 

     _l_e_n_g_t_h 'signature(x = "AffyBatch")': returns the number of
          samples. 

     _p_m_i_n_d_e_x 'signature(object = "AffyBatch")': return the location of
          perfect matches in the intensity matrix.

     _m_m_i_n_d_e_x 'signature(object = "AffyBatch")': return the location of
          the mismatch intensities. 

     _d_i_m 'signature(x = "AffyBatch")': Row and column dimensions.

     _n_c_o_l 'signature(x = "AffyBatch")': An accessor function for
          'ncol'.

     _n_r_o_w 'signature(x = "AffyBatch")': an accessor function for
          'nrow'.

     _n_o_r_m_a_l_i_z_e 'signature(object = "AffyBatch")': a method to
          'normalize'. The method accepts an argument 'method'. The
          default methods is specified in package options (see the main
          vignette).

     _n_o_r_m_a_l_i_z_e._m_e_t_h_o_d_s 'signature(object = "AffyBatch")': returns the
          normalization methods defined for this class. See
          'normalize'.

     _p_r_o_b_e_N_a_m_e_s 'signature(object = "AffyBatch")': returns the probe
          set associated with each row of the intensity matrix. 

     _p_r_o_b_e_s_e_t 'signature(object = "AffyBatch",genenames=NULL,
          locations=NULL)': Extracts 'ProbeSet' objects related to the
          probe sets given in genenames. If an alternative set of
          locations defining pms and mms a list with those locations
          should be passed via the 'locations' argument.

     _b_g._c_o_r_r_e_c_t 'signature(object = "AffyBatch", method="character")'
          applies background correction methods defined by method.

     _u_p_d_a_t_e_O_b_j_e_c_t 'signature(object = "AffyBatch", ...,
          verbose=FALSE)': update, if necessary, an object of class
          AffyBatch to its current class definition. 'verbose=TRUE'
          provides details about the conversion process.

_N_o_t_e:

     This class is better described in the vignette.

_S_e_e _A_l_s_o:

     related methods 'merge.AffyBatch', 'pairs.AffyBatch', and 'eSet'

_E_x_a_m_p_l_e_s:

     if (require(affydata)) {
       ## load example
       data(Dilution)

       ## nice print
       print(Dilution)

       pm(Dilution)[1:5,]
       mm(Dilution)[1:5,]

       ## get indexes for the PM probes for the affyID "1900_at" 
       mypmindex <- pmindex(Dilution,"1900_at")
       ## same operation using the primitive
       mypmindex <- indexProbes(Dilution, which="pm", genenames="1900_at")[[1]]
       ## get the probe intensities from the index
       intensity(Dilution)[mypmindex, ]

       description(Dilution) ##we can also use the methods of eSet
       sampleNames(Dilution)
       abstract(Dilution)
     }

