Changeset 175

Timestamp:

Sep 26, 2006, 11:33:25 AM (17 years ago)

Author:

Johan Enell

Message:

 

File:

• trunk/se/lu/onk/MergeBioAssay/lib/pluginConfiguration.base (modified) (2 diffs)

trunk/se/lu/onk/MergeBioAssay/lib/pluginConfiguration.base

@@ -1 +1 @@
 BASEfile
 section plugin
-uniqueName  onk.lu.se/johan_enell/merge_bioassays2
+uniqueName  onk.lu.se/johan_enell/merge_bioassays
 versionNumber 2.0
-name  Transformation: Merge bioassays 2
+name  Transformation: Merge bioassays
 descr Using this plugin base-users can merge together bioassays by grouping them according to annotation types or syntactical differences in the name. There are four different method for calculating the new values. They differ in what kind of mean they are using (arithmetic or geometric) and if they are merging on ratio or intensity. \r\n\r\nFor each group the parents are saved so the link to the raw data is preserved. Annotations for the bioassays are saved if sample1 is the same for each assay in each group.\r\n\r\nIMPORTANT\r\nIf you have merged assays in a group, BASE 1.2.10 will have difficulties to export data Merged on reporter from the parents RawBioAssays. If you for instance export '[Raw] Spot diameter' for a merged assay, each reporter might be associated with values from several RawBioAssays but only one such value will be exported. This is a known limitation of base 1.2.10 and will be fix in future versions. \r\n\r\nMerge methods\r\n\r\nGeometric mean of ratio:\r\n  This method calculates the geometric mean of the ratios in each group per position.\r\n\r\nArithmetic mean of ratio:\r\n  This method calculates the arithmetic mean of the ratios in each group per position.\r\n\r\nArithmetic mean of intensity:\r\n  This method calculates the arithmetic mean of the intensities in each group per position.\r\n\r\nRatio of ratio:\r\n  This method works a little bit different from the others. It demands that each group consists of exactly two bioassays. Then it will create a new ratio for each spot with one of the assays over the other, depending on what the user has specified in the ratio parameters. \r\n\r\nPARAMETERS:\r\nAssayname\r\nGroup\r\nNew name\r\nMerge method\r\nRatio\r\n\r\n\r\nAssayname - This parameter specifies how the name of the assays is constructed. Use  %0-%9 as wildcards and then put any character(s) between as delimiters. For example assay name Assay_1_A can be divided into three parts. By setting the parameter to %1_%2_%3 the plugin will read assay name assay_1_A and set %1=Assay, %2=1 and %3=A. Thus, if your assays have names constructed in the same way merge can sort the assays in groups depending on %1, %2 or %3.\r\n\r\nGroup - This will specify how the assays will be grouped together. It can either be a %-number used in assayname or an annotation type.\r\n\r\nExample1: Assays; Assay_1_A, Assay_2_A, Assay_1_B and Assay_2_B can be sorted into groups of assays using merge.\r\n \r\n 1a: Setting the parameter \221Assayname\222 = %1_%2_%3 and parameter \221Group\222 = %2 will sort the assays into two groups.\r\n\r\n One group were %2=1 (assays Assay_1_A and Assay_1_B)\r\n One group were %2=2  (assays Assay_2_A and Assay_2_B) \r\n\r\n 1b: Setting the parameter \221Assayname\222 = %1_%2_%3 and parameter \221Group\222 = %3 will sort the assays into two groups.\r\n\r\n One group were %3=A (assays Assay_1_A and Assay_2_A)\r\n One group were %3=B  (assays Assay_1_B and Assay_1_B) \r\n\r\nNew name - This text will be used in the name of the new merged assays. The name will be this string followed by the groupname.\r\n\r\nMerge method - Choose one of the methodes described above.\r\n\r\nRatio - If merge method "ratio of ratio" is chosen the form of the ratio must be specified. This is done either in the ratio parameter or in ratio annotation type and ratio annotation value. In the ratio parameter you can choose a  %-number followed by the two values it can take. The last character in the string must be the delimiter the user has choosen ot use. The other way a user can specify the ratio is by choosing an annotation type in the list and specify the values in the annotation values parameter. This is done by writing the values with the delimiter used last. \r\n\r\nex.\r\n\r\n%1|vr1|vr2|\r\n\r\nThis will take the values from %1 in the assayname and put the assay with value vr1 over the assay with values vr2. Notice that the final character is the delimiter (this can of course be any character).\r\n\r\nExample2: Assays; Assay_1_A, Assay_2_A, Assay_1_B and Assay_2_B can be sorted into groups of assays using merge.\r\n\r\n 1a: Setting the parameter \221Assayname\222 = %1_%2_%3 and parameter \221Group\222  = %2 will sort the assays into two groups.\r\n\r\n One group were %2=1 (assays Assay_1_A and Assay_1_B)\r\n One group were %2=2  (assays Assay_2_A and Assay_2_B)\r\n\r\nBy setting parameter \221Ratio\222 = %3|A|B| ratios of ratios will be created as:\r\n        Assay_1_A / Assay_1_B\r\n        Assay_2_A / Assay_2_B\r\n \r\nArithmetic mean\r\nhttp://mathworld.wolfram.com/ArithmeticMean.html\r\nGeometric mean\r\nhttp://mathworld.wolfram.com/GeometricMean.html\r\n
-execName  onk.lu.se/johane/merge_bioassays2/run
+execName  run
 usedColumns position\treporter
 usedFields  intensity1\tintensity2
@@ -12 +12 @@
 url 
 minChannels 2
-maxChannels 0
+maxChannels 2
 leaveStdin  0
 leaveStdout 0