source: plugins/base1/ @ 2120

Last change on this file since 2120 was 2120, checked in by Jari Häkkinen, 8 years ago

Do not leave stdin/stdout.txt as default

  • Property svn:eol-style set to native
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2section plugin
4versionNumber @VERSION@
5name  Transformation: median/mean centering
6descr To center your data means that you adjust your values to reflect their variation from some property of the data such as the mean or median. The center plugin allows the user to center the expression levels either per gene or per array. Consider a common experimental design where you are looking at a large number of samples all compared to a common reference. For each gene, you have a series of ration values that are relative to the expression level of that gene in the reference sample. Since the reference sample really has nothing  to do with your experiment, you want your analysis to be independent of the amount of a gene present in the reference sample. This is achieved by center your data on genes. Centering makes less sense in experiments where the reference sample is part of the experiment. Centering the data for arrays can also be used to remove certain types of biases and can be seen as a crude normalization. The results of many two-color fluorescent hybridization experiments are not corrected for systematic biases in ratios that are the result of differences in RNA amounts, labeling efficiency and image acquisition parameters. Such biases have the effect of multiplying ratios for all genes by a fixed scalar. Mean or median centering the data in log-space has the effect of correcting this bias, although it should be noted that an assumption is being made in correcting this bias, which is that the average gene in a given experiment is expected to have a ratio of 1.0 (or log-ratio of 0).\r\n\r\nIn general, I recommend the use of median rather than mean centering, as it is more robust against outliers. \r\n\r\n\r\nParameters:\r\n\r\nCenter on genes/arrays - If the centering should be done on genes, arrays or both. If both are chosen then the centering will first be done on genes then on arrays, this is called a cycle. \r\n\r\nAssay groups for centering - If the centering should be based on data in one or more assay groups. If "Default" is selected, centering on arrays is made with each assay in its own group, while centering on genes is made with all assays in one group. "Single assay group" centers all data based on values in a single assay group. "Assay groups" centers each assay group separately. \r\n\r\nCenter group(s) assay names - Comma-separated list of names of assays in groups to use for centering, with each group separated by a '|' character. Only used if "Single assay group" or "Assay groups" has been selected under "Assay groups for centering". \r\n\r\nNumber of centering cycles - How many cycles should be done. This value is only relevant if the centering should be done on both genes and arrays. \r\n\r\nCentering using median or mean - If median or mean should be used for the centering. \r\n\r\nCreate debug files - If debug data should be stored in "data" directory.
7execName  run
8usedColumns position\treporter
9usedFields  l2ratio1_2\tl10intgmean1_2
10geneAverages  0
11serialFormat  0
13minChannels 2
14maxChannels 0
15leaveStdin  0
16leaveStdout 0
17estimatedTime 60
18defaultMaxRam 134217728
19columns position  valueType name  commonName  options defaultValue  enumOptions removed
211 h section   30  center settings   0
222 e centerGeneAssay Center on genes/arrays  30  1 1\tBoth\t2\tArrays (columns)\t3\tGenes (rows) 0
233 e centerAssayGroups Assay groups for centering  30  1 1\tDefault - Arrays: each assay in its own group, genes: all assays in one group\t2\tSingle assay group - Center all data based on values in single assay group\t3\tAssay groups - Center each assay group separately 0
244 t centerGroupsAssayNames  Center group(s) assay names 30      0
255 i centerCycles  Number of centering cycles  10  5   0
266 e mm  Centering using median or mean  30  1 1\tMedian\t2\tMean  0
277 e normGeneAssay Normalize on genes/assays 30  1 1\tBoth\t2\tAssays(columns)\t3\tGenes(rows) 1
288 i normCycles  Number of normalization cycles  10  0   1
299 e createDebugFiles  Create debug files  30  false true\tyes\tfalse\tno  0
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