intensity-methods            package:xps            R Documentation

_G_e_t/_S_e_t _D_a_t_a _V_a_l_u_e_s

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

     Get/set data values from/for class 'DataTreeSet'.

     _Usage_

     'intensity(object)' 
      'intensity(object, filename = NULL, verbose = FALSE) <- value'

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

  object: object of class 'DataTreeSet'.

filename: 'character' vector containing optional ROOT file name.

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

   value: 'data.frame' containing expression values.

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

     Get the intensity values from slot 'data' or set slot 'data' to
     'value'.

     Method 'intensity' returns the data values from slot 'data' as
     'data.frame', while replacement method 'intensity<-' allows to
     replace slot 'data' with a 'data.frame'.

     Using replacement method 'intensity<-' with default settings will
     not change the data stored in the ROOT data file, and thus will
     not have any effect on subsequent processing methods. If you
     really want to use the replacement data for further processing you
     must supply a new ROOT 'filename'. This will export each intensity
     column of 'value' as CEL-file (version 3), which will then be
     imported into the new ROOT data file 'filename'.

     Warning: Do not use replacement method 'intensity<-' until you
     really know what you are doing!

     Note: The first two columns of replacement 'data.frame' 'value'
     must be the (X,Y) coordinates, followed by the intensities whereby
     the number of intensity columns must be identical to the columns
     to be replaced.

     Note: If you do not want to replace your current object, create
     first a copy of type 'DataTreeSet' by simply writing 'newobj <-
     oldobj', and use 'newobj' for replacement. This is important since
     'intensity<-' does also update slots 'rootfile', 'filedir' and
     'treenames' when a new 'filename' was chosen.

     Note: The CEL-files created are fully functional CEL-files
     (version 3), however some header rows such as GridCornerUL,
     AlgorithmParameters, and some of the data in DatHeader are 
     placeholders only.

     Warning: The CEL-files created WILL REPLACE THE ORIGINAL
     CEL-files, if they have identical names to the original CEL-files
     and the original CEL-files are located in the working directory.
     Thus the original CEL-files should preferable be located in
     directory 'celdir' of function 'import.data'.

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

     Christian Stratowa

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

     'validData'

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

     ## Not run: 
     ## 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="/"))

     ## get intensity values
     value <- intensity(data.test3)

     ## make a copy of your object if you do not want to replace it
     newdata.test3 <- data.test3

     ## replace slot data with value
     intensity(newdata.test3, "ReplacementData", FALSE) <- value
     str(newdata.test3)

     ## now you can create an ExprTreeSet using the new intensity data
     data.rma <- rma(newdata.test3,"ReplacementRMA",tmpdir="",background="none",normalize=TRUE,verbose=FALSE)
     ## End(Not run)

