Changeset 828


Ignore:
Timestamp:
Nov 27, 2008, 9:30:02 PM (15 years ago)
Author:
Jari Häkkinen
Message:

Fixes #54

File:
1 edited

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  • plugins/base1/se.lu.thep.wenni/trunk/README

    r825 r828  
    5050= Installation =
    5151
    52 For installation and compilation instructions please read INSTALL.
     52For installation and compilation instructions please read `INSTALL`.
    5353
    5454
    5555= Comments on WeNNI =
    5656
    57 0) WeNNI is presented in the article referenced above.
    58 
    59 1) The notion of weights becomes obsolete after running WeNNI, i.e., do
    60    not use the weight fed into WeNNI in any subsequent analysis
    61    because all weights are now strictly 1.
    62 
    63 2) Running WeNNI as a BASE plug-in makes WeNNI destined to impute log
    64    ratios of channel 1 and channel 2 (M values in BASE world). A
    65    consequence of imputing log ratios is that a change in ratio cannot
    66    be assigned to a specific channel. This implies that
    67    log(channel1*channel2) (A values in BASE world) become undefined
    68    and useless. However, on request from BASE users it was decided
    69    that A values should not be affected by the transformation in cases
    70    where the A value is well defined before imputation. In cases when
    71    an A value do not exist before transformation (i.e. channel1<=0 or
    72    channel2<=0) it was decided that A should be set to 0. NOTE, this
    73    does not change the underlying WeNNI algorithm in any way but is
    74    rather conventions needed for BASE plug-in usage.
    75 
    76 
    77 Remember, if you installed the software as a BASE plug-in, please log
    78 on to the server and make the server aware of the new plug-in. The
    79 plug-in definition file can be found in directory
    80 bin/base_plugin_script as file plugin_WeNNI.base
    81 
    82 
    83 If you installed the software as a standalone package, read on. BASE
    84 plug-in users can also read on if they want some more information
    85 about the WeNNI package. There are three programs created during
    86 compilation:
    87 
    88     BaseFileConverter, NNIFileConverter, nni
    89 
    90 (These files are found in directories ./bin/BaseFileConverter,
    91 ./bin/NNIFileConverter, and ./bin/nni, respectively.)
    92 
    93 
    94 These three programs will take you from a BASE file to an imputed
    95 matrix by running them in the order below (examples 1 to 3). There is
    96 no need to run all steps, i.e., you can generate a data (matrix) file
    97 with an associated weights matrix file and just run nni.
    98 
    99 There is a 4th example below where the wenni.pl script (found in
    100 directory ./bin/base_plugin_script/) is used to run all examples 1
    101 through 3. wenni.pl also generates a resulting BASE file that a BASE
    102 server would accept as a result file (and import it into the database)
    103 when running wenni.pl as a plug-in from within BASE.
    104 
    105 
     57 1. WeNNI is presented in the article referenced above.
     58
     59 2. The notion of weights becomes obsolete after running WeNNI, i.e.,
     60    do not use the weight fed into WeNNI in any subsequent analysis
     61    because all weights are now strictly 1.
     62
     63 3. Running WeNNI as a BASE plug-in makes WeNNI destined to impute log
     64    ratios of channel 1 and channel 2 (M values in BASE world). A
     65    consequence of imputing log ratios is that a change in ratio
     66    cannot be assigned to a specific channel. This implies that
     67    log(channel1*channel2) (A values in BASE world) become undefined
     68    and useless. However, on request from BASE users it was decided
     69    that A values should not be affected by the transformation in
     70    cases where the A value is well defined before imputation. In
     71    cases when an A value do not exist before transformation
     72    (i.e. channel1<=0 or channel2<=0) it was decided that A should be
     73    set to 0. NOTE, this does not change the underlying WeNNI
     74    algorithm in any way but is rather conventions needed for BASE
     75    plug-in usage.
     76
     77 4. Remember, if you installed the software as a BASE plug-in, please
     78    log on to the server and make the server aware of the plug-in. The
     79    BASE1 plug-in definition file can be found in directory
     80    `base/base1/base_plugin_script` as file `plugin_WeNNI.base`. BASE2
     81    users should follow the plug-in installation instructions in the
     82    BASE2 manual available at http://base.thep.lu.se.
     83
     84
     85= WeNNI package details =
     86
     87If you installed the software as a stand alone package two binaries
     88where created `NNIFileConverter` and `nni`. If your input file is a
     89BASEfile you probably want to compile this package in BASE1 mode
     90instead (see `INSTALL` for compilation instructions).
     91
     92The three programs will take you from a BASEfile to an imputed matrix
     93by running them in the order below (examples 1 to 3). There is no need
     94to run all steps, i.e., you can generate a data (matrix) file with an
     95associated weights matrix file and just run `nni` to impute missing
     96values.
     97
     98There is a 4th example below where the `wenni.pl` script (found in
     99directory `./base/base1/base_plugin_script/`) is used to run all
     100examples 1 through 3. `wenni.pl` also generates a result BASEfile that
     101a BASE1 server would accept as a result file (and import it into the
     102database) when running `wenni.pl` as a plug-in from within BASE1.
     103
     104{{{
    1061051) BaseFileConverter.
    107106
    108107   Extracts columns from a file exported from BASE, and writes the
    109108   extracted data into files in matrix form. What data should be
    110    extracted from the BASE file is set by command line options.
     109   extracted from the BASEfile is set by command line options.
    111110
    112111   Command syntax:
    … …  
    122121      <basefile> is the file exported from BASE.
    123122      <string> is a string added to the beginning of all matrix files created.
    124       <fieldtype> defines which field should be extracted from the BASE file.
     123      <fieldtype> defines which field should be extracted from the BASEfile.
    125124      <fieldname> the name of the column to extract.
    126125      ... means that the two last option can be defined several times. This to
    127126          facilitate export of several fields in one run.
    128127
    129       -show will output available fieldtypes and fieldnames in the BASE file.
     128      -show will output available fieldtypes and fieldnames in the BASEfile.
    130129
    131130   Example
    132131 
    133    a) This is an example on how to extract data from a sample BASE
    134       file available in the data directory (data/basefile_in.data)
     132   a) This is an example on how to extract data from a sample BASEfile
     133      available in the data directory (data/basefile_in.data)
    135134
    136135      ./BaseFileConverter basefile_in.data wenni_ -assayFields FCh1Mean \
    … …  
    145144                                 wenni_FCh1Mean.data, wenni_FCh2Mean.data
    146145
    147    b) Another example on how to extract data from a sample BASE file
     146   b) Another example on how to extract data from a sample BASEfile
    148147      available in the data directory (data/basefile_in.data)
    149148
    … …  
    2962954) wenni.pl
    297296
    298    Performs missing value imputation on data in a BASE file. The BASE
    299    file is read from stdin, and the resulting BASE file is written to
    300    stdout. This is how a plug-in is expected to behave to make the
     297   Performs missing value imputation on data in a BASEfile. The
     298   BASEfile is read from stdin, and the resulting BASEfile is written
     299   to stdout. This is how a plug-in is expected to behave to make the
    301300   BASE job runner happy.
    302301
    … …  
    314313                   'derived' (without '' characters). When 'derived'
    315314                   is given, the user defined intensity1 and
    316                    intensity2 will be used from the BASE file. When
     315                   intensity2 will be used from the BASEfile. When
    317316                   'raw' is used, intensity1 will be calculated as
    318317                   FCh1Mean-BCh1Mean (intensity2 is defined
    … …  
    325324
    326325   h) wenni.pl will basically run through examples 1a, 2c, and 3e
    327       sequentially, and produce a BASE file with the imputed
     326      sequentially, and produce a BASEfile with the imputed
    328327      values. 'raw' type of input data is demanded by the command line
    329       options --datatype. Other options are read from the input BASE
    330       file. Intermediate files will not be deleted
     328      options --datatype. Other options are read from the input
     329      BASEfile. Intermediate files will not be deleted
    331330
    332331      ./wenni.pl --datatype raw --nodelete < basefile_in.data > basefile_out.data
    333332
    334333   i) wenni.pl will basically run through examples 1b, 2d, and 3e
    335       sequentially, and produce a BASE file with the imputed
     334      sequentially, and produce a BASEfile with the imputed
    336335      values. 'derived' type of data is expected ('derived' type is
    337       default). Options are read from the input BASE
    338       file. Intermediate files are deleted.
     336      default). Options are read from the input BASEfile.
     337      Intermediate files are deleted.
    339338
    340339      ./wenni.pl < basefile_in.data > basefile_out.data
     340}}}
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