Changeset 879
- Timestamp:
- Dec 5, 2008, 11:28:12 AM (14 years ago)
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plugins/base1/se.lu.onk.Center/trunk/README
r875 r879 3 3 = About `se.lu.onk.Center` = 4 4 5 The `se.lu.onk.Center` plug-in merge bioassays by grouping them 6 according to annotation types or syntactical differences in the 7 name. See ``Documentation`` below fo further information about the 8 plug-in. 5 The `se.lu.onk.Center` plug-in is a normalisation method where 6 expression values are centered around the data median or mean. See 7 ``Documentation`` below for further information about the plug-in. 9 8 10 9 `se.lu.onk.Center` is free software. See the file license.txt for … … 51 50 {{{ 52 51 # Log in to your BASE as admin 53 # Upload the configuration file `mergebioassay.base`52 # Upload the configuration file misc/plugin_Transformation_Center.base` 54 53 # Create/update a configuration for the plug-in where you select the 55 plug-in defin tion files `mergebioassay.base`. BASE will respond56 that plug-ins where configured but ...54 plug-in definition file `plugin_Transformation_Center.base`. BASE 55 will respond that plug-ins where configured but ... 57 56 # Re-configure the plug-in without selecting a file, set the `Plugin 58 57 executables path` and proceed to next window by clicking … … 124 123 == Documentation == 125 124 126 This plug-in base-users merge bioassays by grouping them according to 127 annotation types or syntactical differences in the name. There are 128 four different methods for calculating the merged values. They differ 129 in what kind of mean they are using (arithmetic or geometric) and if 130 they are merging on ratio or intensity. 125 To center your data means that data values are adjusted to reflect 126 their variation from some property of the data such as the mean or 127 median. The center plug-in allows the user to center the expression 128 levels either per gene or per array. 131 129 132 For each group the parents are saved so the link to the raw data is 133 preserved. Annotations for the bioassays are saved if sample1 is the 134 same for each assay in each group. 130 Consider a common experimental design where you are looking at a large 131 number of samples all compared to a common reference. For each gene, 132 you have a series of ratio values that are relative to the expression 133 level of that gene in the reference sample. Since the reference sample 134 really has nothing to do with your experiment, you want your analysis 135 to be independent of the amount of a gene present in the reference 136 sample. This is achieved by center your data on genes. Centering makes 137 less sense in experiments where the reference sample is part of the 138 experiment. 135 139 136 === Merge methods === 140 Centering the data for arrays can also be used to remove certain types 141 of bias and can be seen as a crude normalization. The results of many 142 two-color fluorescent hybridization experiments are not corrected for 143 systematic biases in ratios that are the result of differences in RNA 144 amounts, labeling efficiency, and image acquisition parameters. Such 145 bias have the effect of multiplying ratios for all genes by a fixed 146 scalar. Mean or median centering the data in log-space has the effect 147 of correcting this bias, although it should be noted that an 148 assumption is being made in correcting this bias, which is that the 149 average gene in a given experiment is expected to have a ratio of 1.0 150 (or log-ratio of 0). 137 151 138 ''Geometric mean of ratio'':: 139 This method calculates the geometric mean of the ratios in each 140 group per position. 141 142 ''Arithmetic mean of ratio'':: 143 This method calculates the arithmetic mean of the ratios in each 144 group per position. 145 146 ''Arithmetic mean of intensity'':: 147 This method calculates the arithmetic mean of the intensities in 148 each group per position. 149 150 ''Ratio of ratio'':: 151 This method works a little bit different from the others. It 152 requires that each group consists of exactly two bioassays. It will 153 then create a new ratio for each spot with one of the assays over 154 the other, depending on what the user has specified in the ratio 155 parameters. 152 In general, it is recommended that median rather than mean centering 153 is used since it is more robust against outliers. 156 154 157 155 === Parameters === 158 156 159 ''Assayname'':: 160 This parameter specifies how the name of the assays is 161 constructed. Use %0-%9 as wildcards and then put any character(s) 162 between as delimiters. For example assay name Assay_1_A can be 163 divided into three parts. By setting the parameter to %1_%2_%3 the 164 plugin will read assay name assay_1_A and set %1=Assay, %2=1 and 165 %3=A. Thus, if your assays have names constructed in the same way 166 merge can sort the assays in groups depending on %1, %2 or %3. 157 ''Center on genes/arrays'' - Whether centering should be done on 158 genes, arrays or both. If both is chosen then the centering will first 159 be done on genes then on arrays, this is called a cycle. 167 160 168 '' Group''::169 This will specify how the assays will be grouped together. It can 170 either be a %-number used in assayname or an annotation type.161 ''Number of centering cycles'' - How many cycles should be done during 162 centering. This value is only relevant if the centering should be done 163 on both genes and arrays. 171 164 172 Example 1: Assays; Assay_1_A, Assay_2_A, Assay_1_B and Assay_2_B can 173 be sorted into groups of assays using merge. 174 175 A: Setting the parameter \221Assayname\222 = %1_%2_%3 and parameter 176 \221Group\222 = %2 will sort the assays into two groups. 177 {{{ 178 One group were %2=1 (assays Assay_1_A and Assay_1_B) 179 One group were %2=2 (assays Assay_2_A and Assay_2_B) 180 }}} 181 B: Setting the parameter \221Assayname\222 = %1_%2_%3 and parameter 182 \221Group\222 = %3 will sort the assays into two groups. 183 {{{ 184 One group were %3=A (assays Assay_1_A and Assay_2_A) 185 One group were %3=B (assays Assay_1_B and Assay_1_B) 186 }}} 187 188 ''New name'':: 189 This text will be used in the name of the merged assays. The name 190 will be this string followed by the groupname. 191 192 ''Merge method'':: 193 Choose one of the methodes described above. 194 195 ''Ratio'':: 196 If merge method `ratio of ratio` is chosen the form of the ratio 197 must be specified. This is done either in the ratio parameter or in 198 ratio annotation type and ratio annotation value. In the ratio 199 parameter you can choose a %-number followed by the two values it 200 can take. The last character in the string must be the delimiter the 201 user has choosen ot use. The other way a user can specify the ratio 202 is by choosing an annotation type in the list and specify the values 203 in the annotation values parameter. This is done by writing the 204 values with the delimiter used last, 205 {{{ 206 %1|vr1|vr2| 207 }}} 208 This will take the values from %1 in the assayname and put the assay 209 with value vr1 over the assay with values vr2. Notice that the final 210 character is the delimiter (this can of course be any character). 211 212 Example 2: Assays; Assay_1_A, Assay_2_A, Assay_1_B and Assay_2_B can be 213 sorted into groups of assays using merge. 214 215 A: Setting the parameter \221Assayname\222 = %1_%2_%3 and parameter 216 \221Group\222 = %2 will sort the assays into two groups. 217 {{{ 218 One group were %2=1 (assays Assay_1_A and Assay_1_B) 219 One group were %2=2 (assays Assay_2_A and Assay_2_B) 220 }}} 221 B: By setting parameter \221Ratio\222 = %3|A|B| ratios of ratios 222 will be created as: 223 {{{ 224 Assay_1_A / Assay_1_B 225 Assay_2_A / Assay_2_B 226 }}} 227 228 === References === 229 230 [http://mathworld.wolfram.com/ArithmeticMean.html Arithmetic mean] [[br]] 231 [http://mathworld.wolfram.com/GeometricMean.html Geometric mean] 165 ''Centering using median or mean'' - Whether median or mean should be 166 used for the centering. 232 167 233 168
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