- Timestamp:
- Sep 6, 2011, 8:59:39 AM (11 years ago)
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plugins/base2/net.sf.basedb.illumina/trunk/META-INF/extensions.xml
r1385 r1386 27 27 <about> 28 28 <name>Illumina extensions</name> 29 <version>1.7 pre</version>29 <version>1.7-dev</version> 30 30 <copyright>BASE development team</copyright> 31 31 <email>basedb-users@lists.sourceforge.net</email> 32 32 <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> 34 37 </about> 35 38 <plugin-definition id="Installer"> … … 51 54 This plug-in will remove a per-slide global background from all 52 55 spots. The background is calculated from a set of negative control 53 spots on the array. \n\n56 spots on the array. 54 57 Each assay is treated separately, i.e., no samples are combined 55 58 together. All calculations are made on the current bioassay data 56 59 implying that this plug-in should be used early in analysis and before 57 background spots are removed. \n\n60 background spots are removed. 58 61 A spot is considered to be a negative control spot if it has an 59 ''Control group name'' exactly matching the string ''negative''. \n\n62 ''Control group name'' exactly matching the string ''negative''. 60 63 There is one parameter to set that specifies how background 61 64 intensities should be calculated. Allowed values are median or mean, 62 65 i.e. the background is either the median or the mean of the negative 63 control spots on the array. \n\n66 control spots on the array. 64 67 The expression of the background probes is optionally saved to a 65 68 file. The default is not to save the expression matrix but this can be … … 86 89 Both compressed(gzip) and uncompressed files are supported. 87 90 None of the mappings for the [Controls] section are configurable. 88 These are set like follows: \n89 Identify features by->FEATURE_ID \nReporter ID->\\Probe_Id\\\nFeature ID->\\Array_Address_Id\\\n91 These are set like follows: 92 Identify features by->FEATURE_IDReporter ID->\\Probe_Id\\Feature ID->\\Array_Address_Id\\ 90 93 Reg exp for data header is preconfigured to 'Probe_Id\\tArray_Address_Id.*' 91 94 </description> … … 114 117 <description> 115 118 This plug-in implements BeadStudio like detection P-value calculations 116 for Illumina expression data. \n\n119 for Illumina expression data. 117 120 The plug-in will _always_ base the detection P-value calculation on 118 121 raw data values, i.e., the mean raw intensity for the different … … 120 123 available in the root bioassay set for the current analysis 121 124 branch. The user may change this to only use negative controls in the 122 current bioassay set. \n\n125 current bioassay set. 123 126 The detection P-value plug-in does not filter the assays, it provides 124 127 the detection P-values usable in a filter step after running this 125 plug-in. \n\n126 Parameters \n128 plug-in. 129 Parameters 127 130 - The plug-in requires input of array type since detection P-value are 128 calculated differently depending on array type. \n131 calculated differently depending on array type. 129 132 - Users may select to use negative controls in the current bioassay set 130 133 only. The default behaviour is to use all negative controls in the 131 root bioassay set for the current bioassay set. \n134 root bioassay set for the current bioassay set. 132 135 - A cut off parameter is available to exclude outliers within 133 136 the negative controls. The `cutoff` defines the acceptable negative 134 137 control signal range 135 138 $median-MAD*cutoff < I < median+MAD*cutoff$ 136 where $MAD$ is the median absolute deviation. \n\n137 Implementation details \n\n139 where $MAD$ is the median absolute deviation. 140 Implementation details 138 141 Each assay is treated separately, i.e., no samples are combined 139 142 together. All calculations are made on the raw bead-type level data, 140 143 i.e., on the average expression value for each bead type and raw data 141 144 is always used irrespective when in analysis the detection P-value is 142 calculated. \n\n143 Pvalue calculation for whole genome arrays: \n145 calculated. 146 Pvalue calculation for whole genome arrays: 144 147 For all signals $i$ calculate the detection P-value as 145 148 $Pvalue = 1-R/N$ where $R$ is the rank of the signal $i$ relative to the 146 negative controls and $N$ is the number of negative controls. \n\n149 negative controls and $N$ is the number of negative controls. 147 150 Pvalue calculation for others array types (DASL, miRNA, VeraCode DASL, 148 and Focused Arrays): \n151 and Focused Arrays): 149 152 For all signals $i$ calculate the detection P-value as 150 153 $Pvalue = 1/2 - 1/2 * erf( [i-AvgControl]/StdControl/sqrt(2) )$ where … … 155 158 for arguments within the range (-4,4). To save CPU cycles, the function 156 159 value for arguments outside this range is set to -1 and 1, 157 respectively. \n\n160 respectively. 158 161 More details about this plug-in is found at the URL 159 \n\nPlease send feedback to the email-address162 Please send feedback to the email-address 160 163 </description> 161 164 </about> … … 169 172 only if all raw bioassays has the same array design and SNP split data files 170 173 are present. The root bioassayset is created by copying values from the data files 171 as follows: \n172 * Channel 1 = GType (AA = 1.0, AB = 0.0, BB = -1.0, NC = null \n173 * Channel 2 = Log R Ratio \n174 as follows: 175 * Channel 1 = GType (AA = 1.0, AB = 0.0, BB = -1.0, NC = null) 176 * Channel 2 = Log R Ratio 174 177 * Channel 3 = B Allele Freq 175 178 </description> … … 215 218 </action-factory> 216 219 </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> 256 217 257 </extensions>
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