read.madata             package:maanova             R Documentation

_R_e_a_d _M_i_c_r_o _A_r_r_a_y _d_a_t_a _f_r_o_m _T_A_B _d_e_l_i_m_i_t_e_d _s_i_m_p_l_e _t_e_x_t _f_i_l_e

_D_e_s_c_r_i_p_t_i_o_n:

     This is the function to read MicroArray experiment data from a TAB
      delimited simple text file.

_U_s_a_g_e:

     read.madata(datafile, designfile="design.txt", header=TRUE, spotflag=TRUE,
                 metarow, metacol, row, col, pmt, ...)

_A_r_g_u_m_e_n_t_s:

datafile: The data file name with path name as a string.

designfile: The design file name with path as a string.

  header: A logical value indicating whether the data file contains the
          column headers.

spotflag: A flag to indicate whether the input file contain the flag
          for bad spot or not.

 metarow: The column number for meta row. Default values are 1s.

 metacol: The column number for meta column. Default values are 1s.

     row: The column number for row. Default value is NA.

     col: The column number for column. Default value is NA.

     pmt: The start column number for pmt data.

     ...: Other gene information in the data file.

_V_a_l_u_e:

     An object of class 'rawdata', which is a list of following
     components: 

 n.array: Number of arrays in the experiment.

   n.dye: Number of dyes.

    data: Two channel experiment data.

    flag: A matrix for spot flag. Each element corresponding to one
          spot. 0 means normal spot, all other values mean bad spot.

 metarow: Meta row for each spot.

 metacol: Meta column for each spot.

     row: Row for each spot.

     col: Column for each spot.

ArrayName: A list of strings to represent the names of the pmt data.
          There are two names per array.

  design: An object to represent the experimental design.

  Others: Other experiment information listed in the data file and
          specified by user.

_P_r_e_p_a_r_i_n_g _d_a_t_a _f_i_l_e:

     Before using the package, user need to prepare the input data
     file. The data file is a TAB delimited text file. In this file,
     each row corresponding to a gene. In the columns, you can put some
     gene specific information, e.g., the Clone ID, Gene Bank ID, etc.
     and the grid location of the spot. But most importantly you need
     to put the pmt data after that. Most of the MicroArray gridding
     softwares generate one file for each slide. At this point, you
     need to manually combine them into the data file. You need to
     decide which data you want to use in analysis, e.g., mean versus
     median, backgroud subtracted or not, etc. For N-dye array, your
     pmt data should have N columns for each array.  These N columns
     need to be adjacent to each other. You can put the spot flag as a
     column after pmt data for each array. (Note that if you have flag,
     you will have N+1 columns data for each array.) If you have
     replicates, replicated measurements of the same clone on the same
     array should appear in adjacent rows.   

     For example, for a 2-dye cDNA array, you have four slides scanned
     by Gene Pix and you get four files. First you open your favorite
     Spreed Sheet editor, e.g., MS Excel. Copy your clone ID and
     Cluster ID to the first 2 columns. Then open one of the files
     generated by Gene Pix, copy the grid location into next 4 columns
     (you only need to do this once because they are all the same for
     four slides). Then for all four files, copy the two columns of
     foreground median value (if you want to use it) and one column of
     flag to the file in the order of Cy5, Cy3, flag. Then select the
     whole file and row sort it according to Clone ID. Save the file as
     tab delimited text file and you are done.

     The data file must be "full", that is, all rows have to have same
     number of fields. Sometimes leading and trailing TAB in the text
     file will bring problems, depends on the operating system. So user
     need to be careful about that.

_P_r_e_p_a_r_i_n_g _d_e_s_i_g_n _f_i_l_e:

     Design file is another TAB delimited text file. Number of rows of
     this file equals number of arrays times N (the number of dyes).
     Number of columns of this file depends on the experimental design.
     For example, you can have "Strain", "Diet", "Sex", etc. in your
     design file. You *MUST* have a column named "Sample" (case
     sensitive) in the design file. It should be  integers to represent
     the biological individuals. Reference samples should have Sample
     number to be zero(0). Reference sample will always be treated as
     fixed factor in mixed model and it will not be involved in any
     test. You also must have "Array" and "Dye" columns in the design
     file. You must NOT have "Spot" and "Label" columns. They are
     reserved for spotting and labelling effects. 

     Note that you don't have to *USE* all factors in design file. In
     making the model object in 'makeModel', the experimental design
     will be determined by the design and a formula. You can put all
     factors in design file but turn them on/off in formula.

_R_e_a_d _p_r_e-_t_r_a_n_s_f_o_r_m_e_d _d_a_t_a:

     You can use other softwares to do data transformation and read in
     the pre-transformed data into R/maanova. If that is the case, you
     should skip the log2 transformation in 'createData' by setting
     log.trans=FALSE. And you should do 'riplot' and 'arrayview' on the
     result of 'createData'. Because 'riplot' and 'arrayview' assume
     the data in 'rawdata' object is on raw scale.

_A_u_t_h_o_r(_s):

     Hao Wu

_E_x_a_m_p_l_e_s:

     # note that data files are not distributed with the package,
     # read in a file with spot flag
     ## Not run: 
     kidney.raw <- read.madata("kidney.txt", designfile="kidneydesign.txt", 
             metarow=1, metacol=2, col=3, row=4, Name=5, ID=6,
             pmt=7, spotflag=TRUE)
     ## End(Not run)
     # read in a file without spot flag
     ## Not run: 
     rawdata <- read.madata("paigen.txt", designfile="design.txt",cloneid=1, 
             metarow=2, metacol=3, row=4, col=5, pmt=6, spotflag=FALSE)
     ## End(Not run)

