cellHTS-class            package:cellHTS2            R Documentation

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_p_e_r_f_o_r_m_e_d _i_n _p_l_a_t_e _f_o_r_m_a_t.

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

     Container for data and experimental meta-data from cell-based
     high-throughput assays performed in plate format. Typical
     applications are RNA interference or small molecular compound
     screens. The class extends the 'NChannelSet' class. Data are from
     experiments where the same set of reagents (probes) where used. 
     The class can represent data from multi-channel assays.

     The data can be thought of as being organised in a two- or
     three-dimensional array as follows:

        *  The first dimension corresponds to reagents (e.g. siRNAs,
           chemical compounds) that were used in the assays. For
           example, if the screen used 100 plates of 384 wells (24
           columns, 16 rows), then the first dimension has size 38,400,
           and the 'cellHTS' object keeps track of plate ID, row, and
           column associated with each element. For historic reasons,
           and because we are using infrastructure that was developed
           for microarray experiments, the following terms are used
           synonymously for the elements of the first dimension:
           reagents, features, probes, genes.

        *  The second dimension corresponds to assays, including
           replicates and different experimental conditions (cell type,
           treatment, genetic background). A potentially confusing
           terminology is that the data structure that annotates the
           second dimension is called 'phenoData'. This is because we
           are using infrastructure (the 'NChannelSet' class) that uses
           this unfortunate term for this purpose. The software
           provides methodology for replicate summarization and
           scoring, however more complicated experimental designs are
           not directly supported. Multi-purpose tools like 'lmFit' in
           the 'limma' package should be consulted.

        *  The (optional) third dimension corresponds to different
           channels (e.g. different luminescence reporters)    

_O_b_j_e_c_t_s _f_r_o_m _t_h_e _C_l_a_s_s:

     Objects can be created by calls of the form 'new("cellHTS",
     assayData, phenoData, ...)'. See the examples below.

_S_l_o_t_s:



     '_p_l_a_t_e_L_i_s_t': a 'data.frame' containing what was read from input
          measurement data files plus a column 'status' of type
          character containing the string "OK" if the data import
          appeared to have gone well, and the respective error or
          warning message otherwise.

     '_i_n_t_e_n_s_i_t_y_F_i_l_e_s': a list, where each component contains a copy of
          the imported input data files. Its length corresponds to the
          number of rows of 'plateList'.  

     '_s_t_a_t_e': a logical vector of length 4 representing the processing
          status of the object. It must have the names "configured",
          "normalized", "scored" and "annotated".  

     '_p_l_a_t_e_C_o_n_f': a 'data.frame' containing what was read from the
          _configuration file_ for the experiment (except the first two
          header rows). It contains at least three columns named
          'Plate', 'Well' and 'Content'. Columns 'Plate' and 'Well' are
          allowed to contain regular expressions.  

     '_s_c_r_e_e_n_L_o_g': a 'data.frame' containing what was read from the
          _screen log file_ for the experiment, in case it exists.
          Contains at least three columns, and column names 'Plate',
          'Well', and 'Flag'. Additional columns are 'Sample' (when
          there are replicates or more than one sample or condition)
          and 'Channel' (when there are multiple channels).  

     '_s_c_r_e_e_n_D_e_s_c': a character containing what was read from the
          _description file_ of the experiment.  

     '_b_a_t_c_h': a 3D-array with the first two dimensions corresponding to
          the dimension of each matrix in 'assayData' slot and the
          third dimension corresponding to the number of channels in
          'assayData' slot (Features x Samples x Channels). Should
          contain integer values giving the batch number (1, 2, ...)
          for each plate, sample and channel.  

     '_r_o_w_c_o_l._e_f_f_e_c_t_s': a 3D array of size Features (i.e. plate size x
          number of plates) x Samples x Channels containing estimated
          row and column plate spatial offsets.  

     '_o_v_e_r_a_l_l._e_f_f_e_c_t_s': a 3D array of size Features x Samples x
          Channels containing estimated plate overall offsets.

     '_a_s_s_a_y_D_a_t_a': Object of class 'AssayData', usually an environment
          containing matrices of identical size. Each matrix represents
          a single channel. Columns in each matrix correspond to
          samples (or replicate), rows to features (probes).  Once
          created, 'cellHTS' manages coordination of samples and
          channels.  

     '_p_l_a_t_e_D_a_t_a': A list of data frames, with number of rows of each
          frame equal to the number of plates used in the assay and
          number of columns equal to the number of samples. Each data
          frame in the list should contain factorial annotation
          information relevant for the individual plates, like
          experimental batches or varying types of micro-titre plates.
          Currently, this information will be used for between-batch
          normalization and quality assessment.  

     '_p_h_e_n_o_D_a_t_a': Object of class 'AnnotatedDataFrame'. Please see the
          documentation of the 'phenoData' slot of 'NChannelSet' for
          more details.

          It contains information about the screens, and it must have
          the following columns in its 'data' component: 'replicate'
          and 'assay', where 'replicate' is expected to be a vector of
          integers giving the replicate number, while 'assay' is
          expected to be a vector of characters giving the name of the
          biological assay. Both of these vectors should have the same
          length as the number of Samples.

          Once created, 'cellHTS' coordinates selection and subsetting
          of channels in 'phenoData'.  

     '_f_e_a_t_u_r_e_D_a_t_a': Object of class 'AnnotatedDataFrame', containing
          information about the reagents: plate, well, column, the well
          annotation (sample, control, etc.), etc.  For a 'cellHTS'
          object, this slot must contain in its 'data' component at
          least three mandatory columns named 'plate', 'well' and
          'controlStatus'. Column 'plate' is expected to be a numeric
          vector giving the plate number (e.g. 1, 2, ...), 'well'
          should be a vector of characters (alphanumeric characters)
          giving the well ID within the plate (e.g. A01, B01, H12,
          etc.).  Column 'controlStatus' should be a factor specifying
          the annotation for each well with possible levels: _empty_,
          _other_, _neg_, _sample_, and _pos_. Other levels besides
          _pos_ and _neg_ may be employed for controls.  

     '_e_x_p_e_r_i_m_e_n_t_D_a_t_a': Object of class 'MIAME' containing descriptions
          of the experiment.

     '_a_n_n_o_t_a_t_i_o_n': A '"character"' of length 1, which can be used to
          specify the name of an annotation package that goes with the
          reagents used for this experiment.

     '.___c_l_a_s_s_V_e_r_s_i_o_n__': Object of class 'Versions', containing
          automatically created information about the class definition,
          Biobase package version, and other information about the user
          system at the time the instance was created. See
          'classVersion' and 'updateObject' for examples of use.  


_E_x_t_e_n_d_s:

     Class 'NChannelSet', directly.

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

     Methods with class-specific functionality:



     '_n_a_m_e(_o_b_j_e_c_t)' 'signature(object="cellHTS")'. Obtains the name of
          the assay stored in the 'object'. This corresponds to the
          contents of column 'assay' of the 'phenoData' slot of the
          'cellHTS' object.  

     '_n_a_m_e(_o_b_j_e_c_t) <- _v_a_l_u_e' 'signature(object = "cellHTS", value =
          "character")' assign the character of length one ('value') to
          the elements in column 'assay' of the slot 'phenoData' of
          'object'.  

     '_p_d_i_m(_o_b_j_e_c_t)' 'signature(object = "cellHTS")'. Obtain the plate
          dimension for the data stored in 'object'.


     '_n_b_a_t_c_h(_o_b_j_e_c_t)' 'signature(object = "cellHTS")'. Obtain the total
          number of batches for the data stored in 'object'.


     '_c_o_m_p_a_r_e_2_c_e_l_l_H_T_S(_x, _y)' 'signature(x = "cellHTS", y = "cellHTS")'.
           Compares two 'cellHTS' objects, 'x' and 'y', returning
          'TRUE' if they are from the same experiment (i.e. if they
          derive from the same initial 'cellHTS' object), or 'FALSE'
          otherwise.  


     Methods with functionality derived from class 'NChannelSet':
     'channel', 'channelNames', 'selectChannels', 'object[features,
     samples]', 'sampleNames'

     Methods with functionality derived from 'eSet': 'annotation',
     'assayData', 'assayData<-', 'classVersion', 'classVersion<-',
     'dim', 'dims', 'experimentData', 'featureData', 'phenoData',
     'phenoData<-', 'pubMedIds', 'sampleNames', 'sampleNames<-',
     'storageMode', 'varMetadata', 'isCurrent', 'isVersioned'.

     Additional methods: 


     '_i_n_i_t_i_a_l_i_z_e' used internally for creating objects

     '_s_h_o_w' invoked automatically when the object is displayed to the
          screen. It prints a summary of the object.

     '_s_t_a_t_e' Access the 'state' slot of a 'cellHTS' instance.

     '_a_n_n_o_t_a_t_e' Annotate the 'cellHTS' object using the _screen
          annotation file_.

     '_c_o_n_f_i_g_u_r_e' Configure the 'cellHTS' object using the the _screen
          description file_, the _screen configuration file_ and the
          _screen log file_.

     '_w_r_i_t_e_T_a_b' Write the contents of 'assayData' slot of a 'cellHTS'
          object to a tab-delimited file.

     '_R_O_C' Construct an object of S4 class 'ROC', which represents a
          receiver-operator-characteristic curve, from the data of the
          annotated positive and negative controls in a scored
          'cellHTS' object.

     '_m_e_a_n_S_d_P_l_o_t(_x)' 'signature(x = "cellHTS")' plots row standard
          deviations across samples versus row means across samples for
          data stored in slot 'assayData' of a 'cellHTS' object. If
          there are multiple channels, row standard deviations and row
          means are calculated across samples for each channel
          separately. Only wells containing "sample" are considered.
          See 'meanSdPlot' for more details about this function.


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

     Ligia P. Bras ligia@ebi.ac.uk, Wolfgang Huber huber@ebi.ac.uk

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

     'NChannelSet' 'readPlateList' 'annotate' 'configure' 'writeTab'
     'state' 'Data' 'normalizePlates' 'ROC'

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

         showClass("cellHTS")
         showMethods(class="cellHTS")
       
         ## An empty cellHTS
         obj <- new("cellHTS")

         data("KcViabSmall")
         KcViabSmall
         state(KcViabSmall)
         ## Replicate 1 as a cellHTS object
         y <- KcViabSmall[,1] 
         compare2cellHTS(KcViabSmall, y)
         data("KcViab")
         compare2cellHTS(KcViab, KcViabSmall)

