Ignore:
Timestamp:
Sep 6, 2011, 8:59:39 AM (11 years ago)
Author:
Nicklas Nordborg
Message:

Fixes #311: Updates required for BASE 3 support

BGX and SNP manifest file validation seems to be working. Updated readme and installation instructions.

File:
1 edited

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  • plugins/base2/net.sf.basedb.illumina/trunk/META-INF/extensions.xml

    r1385 r1386  
    2727  <about>
    2828    <name>Illumina extensions</name>
    29     <version>1.7pre</version>
     29    <version>1.7-dev</version>
    3030    <copyright>BASE development team</copyright>
    3131    <email>basedb-users@lists.sourceforge.net</email>
    3232    <url>http://baseplugins.thep.lu.se/wiki/net.sf.basedb.illumina</url> 
    33     <minbaserversion>3.0</minbaserversion> 
     33    <description>
     34      This package contains plug-ins and extensions for the Illumina platform.
     35    </description>
     36    <min-base-version>3.0.0</min-base-version>
    3437  </about>
    3538  <plugin-definition id="Installer">
     
    5154        This plug-in will remove a per-slide global background from all
    5255        spots. The background is calculated from a set of negative control
    53         spots on the array.\n\n
     56        spots on the array.
    5457        Each assay is treated separately, i.e., no samples are combined
    5558        together. All calculations are made on the current bioassay data
    5659        implying that this plug-in should be used early in analysis and before
    57         background spots are removed.\n\n
     60        background spots are removed.
    5861        A spot is considered to be a negative control spot if it has an
    59         ''Control group name'' exactly matching the string ''negative''.\n\n
     62        ''Control group name'' exactly matching the string ''negative''.
    6063        There is one parameter to set that specifies how background
    6164        intensities should be calculated. Allowed values are median or mean,
    6265        i.e. the background is either the median or the mean of the negative
    63         control spots on the array.\n\n
     66        control spots on the array.
    6467        The expression of the background probes is optionally saved to a
    6568        file. The default is not to save the expression matrix but this can be
     
    8689        Both compressed(gzip) and uncompressed files are supported.
    8790        None of the mappings for the [Controls] section are configurable.
    88         These are set like follows:\n
    89         Identify features by->FEATURE_ID\nReporter ID->\\Probe_Id\\\nFeature ID->\\Array_Address_Id\\\n
     91        These are set like follows:
     92        Identify features by->FEATURE_IDReporter ID->\\Probe_Id\\Feature ID->\\Array_Address_Id\\
    9093        Reg exp for data header is preconfigured to 'Probe_Id\\tArray_Address_Id.*'
    9194      </description>
     
    114117      <description>
    115118        This plug-in implements BeadStudio like detection P-value calculations
    116         for Illumina expression data.\n\n
     119        for Illumina expression data.
    117120        The plug-in will _always_ base the detection P-value calculation on
    118121        raw data values, i.e., the mean raw intensity for the different
     
    120123        available in the root bioassay set for the current analysis
    121124        branch. The user may change this to only use negative controls in the
    122         current bioassay set.\n\n
     125        current bioassay set.
    123126        The detection P-value plug-in does not filter the assays, it provides
    124127        the detection P-values usable in a filter step after running this
    125         plug-in.\n\n
    126         Parameters\n
     128        plug-in.
     129        Parameters
    127130        - The plug-in requires input of array type since detection P-value are
    128         calculated differently depending on array type.\n
     131        calculated differently depending on array type.
    129132        - Users may select to use negative controls in the current bioassay set
    130133        only. The default behaviour is to use all negative controls in the
    131         root bioassay set for the current bioassay set.\n
     134        root bioassay set for the current bioassay set.
    132135        - A cut off parameter is available to exclude outliers within
    133136        the negative controls. The `cutoff` defines the acceptable negative
    134137        control signal range
    135138        $median-MAD*cutoff &lt; I &lt; median+MAD*cutoff$
    136         where $MAD$ is the median absolute deviation.\n\n
    137         Implementation details\n\n
     139        where $MAD$ is the median absolute deviation.
     140        Implementation details
    138141        Each assay is treated separately, i.e., no samples are combined
    139142        together. All calculations are made on the raw bead-type level data,
    140143        i.e., on the average expression value for each bead type and raw data
    141144        is always used irrespective when in analysis the detection P-value is
    142         calculated.\n\n
    143         Pvalue calculation for whole genome arrays:\n
     145        calculated.
     146        Pvalue calculation for whole genome arrays:
    144147        For all signals $i$ calculate the detection P-value as
    145148        $Pvalue = 1-R/N$ where $R$ is the rank of the signal $i$ relative to the
    146         negative controls and $N$ is the number of negative controls.\n\n
     149        negative controls and $N$ is the number of negative controls.
    147150        Pvalue calculation for others array types (DASL, miRNA, VeraCode DASL,
    148         and Focused Arrays):\n
     151        and Focused Arrays):
    149152        For all signals $i$ calculate the detection P-value as
    150153        $Pvalue = 1/2 - 1/2 * erf( [i-AvgControl]/StdControl/sqrt(2) )$ where
     
    155158        for arguments within the range (-4,4). To save CPU cycles, the function
    156159        value for arguments outside this range is set to -1 and 1,
    157         respectively.\n\n
     160        respectively.
    158161        More details about this plug-in is found at the URL
    159         \n\n Please send feedback to the email-address
     162        Please send feedback to the email-address
    160163      </description>
    161164    </about>   
     
    169172        only if all raw bioassays has the same array design and SNP split data files
    170173        are present. The root bioassayset is created by copying values from the data files
    171         as follows:\n
    172          * Channel 1 = GType (AA = 1.0, AB = 0.0, BB = -1.0, NC = null\n
    173          * Channel 2 = Log R Ratio\n
     174        as follows:
     175         * Channel 1 = GType (AA = 1.0, AB = 0.0, BB = -1.0, NC = null)
     176         * Channel 2 = Log R Ratio
    174177         * Channel 3 = B Allele Freq
    175178      </description>
     
    215218    </action-factory>
    216219  </extension>
     220  <extension
     221    id="net.sf.basedb.illumina.extensions.bgxvalidator"
     222    extends="net.sf.basedb.core.filehandler.validator"
     223    >
     224    <about>
     225      <name>BGX file validator</name>
     226      <description>
     227        Validator and metadata extractor implementation for Illumina BGX files.
     228        It will parse the start of the file until the [Probes] section is found
     229        and then extract the number of probes + controls and set that as the
     230        number of features on the array design.
     231      </description>
     232    </about>
     233    <index>1</index>
     234    <action-factory>
     235      <factory-class>net.sf.basedb.illumina.filehandler.BgxValidationFactory</factory-class>
     236    </action-factory>
     237  </extension>
     238  <extension
     239    id="net.sf.basedb.illumina.extensions.snpvalidator"
     240    extends="net.sf.basedb.core.filehandler.validator"
     241    >
     242    <about>
     243      <name>SNP manifest validator</name>
     244      <description>
     245        Validator and metadata extractor implementation for Illumina SNP manifest files.
     246        It will parse the start of the file until the [Assay] section is found
     247        and then extract the SNP Count value and set that as the number of features
     248        on the array design.
     249      </description>
     250    </about>
     251    <index>1</index>
     252    <action-factory>
     253      <factory-class>net.sf.basedb.illumina.filehandler.SnpCvsValidationFactory</factory-class>
     254    </action-factory>
     255  </extension>
     256 
    217257</extensions>
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