NAME

RAD::DataLoad::Plugin::RmarrayNormalizer - Loess normalize two-channel cDNA array data using the R marray package from BioConductor (possibly after removing flagged spots).


SYNOPSIS

ga RAD::DataLoad::Plugin::RmarrayNormalizer --help

ga RAD::DataLoad::Plugin::RmarrayNormalizer --helpHTML

ga RAD::DataLoad::Plugin::RmarrayNormalizer --cfg_file file --qid1 integer --qid2 integer --fg string [--bg string] [--print_tip ] [--smoothing_param float] [--commit ] [--debug ] [--sqlVerbose ] [--verbose ] [--veryVerbose ] [--user string] [--group string] [--project string] [--comment string] [--algoinvo integer] [--gusconfigfile file]


DESCRIPTION

This plugin takes in 2 related quantification_id's of a cDNA assay and performs loess normalization on the raw data using the R marray package. If the data were originally quantified with GenePix, the option of removing elements with specified flags prior to this normalization can also be exercised. The plugin creates an entry in RAD3.LogicalGroup and 2 entries in RAD3.LogicalGroupLink and outputs a data and config file which can be used with GUS::RAD::Plugin::AnalysisResultLoader to load the normalized data into table RAD3.DataTransformationResult.


TABLES AFFECTED

RAD3::LogicalGroup

Enters a row which will be used as analysis input for this normalization process

RAD3::LogicalGroupLink

Enters 2 rows which correspond to the 2 input quantifications

Core::AlgorithmInvocation

The plugin manager (ga) inserts a row into this table describing the plugin and the parameter values used


TABLES DEPENDED ON

RAD3::Protocol

The analysis protocol used

RAD3::ProtocolParam

The parameters for the protocol or its components

Core::TableInfo

The table from which the table_id for RAD3.Quantification is retrieved

Core::DatabaseInfo

The table from which the database_id for RAD3 is retrieved

Core::Algorithm

The algorithm (ie, this plugin) responsible for the update

Core::AlgorithmImplementation

The specific implementation of it

Core::AlgorithmParamKey

The keys for the plugin's command line parameters

Core::AlgorithmParamKeyType

The data types of the parameters


ARGUMENTS IN DETAIL

--cfg_file file (Required)

The full path of the cfg_file.

format: See the NOTES for the format of this file
mustExist: 1
--qid1 integer (Required)

quantification_id 1 for the channel to be used as the numerator in loess normalization.

--qid2 integer (Required)

quantification_id 2 for the channel to be used as the denominator in loess normalization.

--fg string (Required)

The name of the field to be used as foreground measurement; should be one of the foreground fields of the view of RAD3.ElementResultImp into which the quantifications were loaded.

--bg string

The name of the field to be used as background measurement. If specified, background subtraction will be performed. In this case, this argument should be one of the background fields of the view of RAD3.ElementResultImp into which the quantifications were loaded.

--print_tip

If specified, print-tip loess will be used instead of global loess.

--smoothing_param float

The smoother span.

default: 0.4
--commit

Actualy commit changes to the database

default: 0
--debug

output extra debugging information to verify correct operation

default: 0
--sqlVerbose

Use this flag to switch on a log of SQL statements executed by Perl object layer.

default: 0
--verbose

Use this flag to enable output of logVerbose messages from the plugin.

default: 0
--veryVerbose

Use this flag to enable output of logVeryVerbose and logVerbose messages from the plugin.

default: 0
--user string

Set the user name in new or changed rows with this GUS user name (from Core.UserInfo table) [default is value in gus config file]

--group string

Set the group name in new or changed rows with this GUS group name (from Core.GroupInfo table) [default is value in gus config file]

--project string

set the project name in new or changed rows with this GUS project name (from Core.Project table) [default is value in gus config file]

--comment string

Set Core.AlgorithmInvocation.comment with this comment

--algoinvo integer

Use this algorithm invocation id in the event that a new algorithm invocation id cannot be generated automatically

default: 1
--gusconfigfile file

The gus config file to use [note: the default is your $GUS_CONFIG_FILE]

default: /home/manduchi/.gus.properties
format: GUS config file format
mustExist: 1
--help

Request long help

--helpHTML

Request help in HTML


NOTES

cfg_file

In this file the field element_result_table should always be provided. The flag fields should only be provided if one wants to remove flagged elements before loess normalization (currently this option is available only if the input data were quantified with GenePix).

This should be a tab-delimited text file with 2 columns: name and value.

Comment lines should start with #.

Each (non-comment) line should contain exactly one tab.

The required names are as follows:

element_result_table The specific view of RAD3.ElementResultImp to which the element result data after quantification are loaded. FOR NOW THIS IS LIMITED TO GenePixElementResult.

The following parameters are optional:

flag_nameN The name of the Nth flag in the specified element_result_table which will be used to exclude elements whose flag value equals flag_valueN. FOR NOW THIS IS LIMITED TO flag (from RAD3.GenePixElementResult)

flag_valueN The value specified for the flagN.

See the sample config file sample_RmarrayNormalizer.cfg in the $PROJECT_HOME/RAD/DataLoad/config directory.


AUTHOR

Written by Hongxian He.


COPYRIGHT

Copyright Hongxian He, Trustees of University of Pennsylvania 2005.