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12 Jan 06 |
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BASEfile |
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section plugin |
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26 Sep 06 |
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uniqueName onk.lu.se/johan_enell/merge_bioassays |
| 776 |
18 Sep 08 |
jari |
versionNumber @VERSION@ |
| 175 |
26 Sep 06 |
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name Transformation: Merge bioassays |
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12 Jan 06 |
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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 |
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26 Sep 06 |
enell |
execName run |
| 60 |
12 Jan 06 |
enell |
usedColumns position\treporter |
| 60 |
12 Jan 06 |
enell |
usedFields intensity1\tintensity2 |
| 60 |
12 Jan 06 |
enell |
geneAverages 0 |
| 60 |
12 Jan 06 |
enell |
serialFormat 0 |
| 898 |
08 Dec 08 |
jari |
url http://baseplugins.thep.lu.se/wiki/se.lu.onk.MergeBioAssay |
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12 Jan 06 |
enell |
minChannels 2 |
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26 Sep 06 |
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maxChannels 2 |
| 60 |
12 Jan 06 |
enell |
leaveStdin 0 |
| 60 |
12 Jan 06 |
enell |
leaveStdout 0 |
| 60 |
12 Jan 06 |
enell |
columns position valueType name commonName options defaultValue enumOptions removed |
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12 Jan 06 |
enell |
18 |
% |
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12 Jan 06 |
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1 h section newname 10 merge_bioassays settings 0 |
| 60 |
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2 t assayname assayname 10 %1 0 |
| 60 |
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3 t group Group 10 %1 0 |
| 60 |
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4 t newname newname 10 0 |
| 60 |
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5 e mergeMethod Merge method 30 0 0\tgeometric mean of ratio\t1\tarithmetric mean or ratio\t2\tarithmetric mean or intensity\t3\tratio of ratio 0 |
| 60 |
12 Jan 06 |
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6 t ratio - Ratio (ignored if merge method is other than 'ratio of ratio') 10 0 |
| 60 |
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7 n annType -- Ratio annotation type 30 0 0 |
| 60 |
12 Jan 06 |
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8 t annValue --- Ratio annotaion value (ignored unless a Ratio annotation type is selected) 10 0 |
| 60 |
12 Jan 06 |
enell |
27 |
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