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BASEfile |
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section plugin |
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uniqueName onk.lu.se/johane/lowess |
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versionNumber 2.0 |
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name Normalization: Lowess v2.0 |
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descr This is an update of the Normalization: Lowess plug-in implemented by Johan Enell <johan.enell\@onk.lu.se>. It is based on the LOWESS algorithm implemented by Bj\366rn Samuelsson <bjorn.samuelsson\@thep.lu.se.\r\n\r\nThe window size is the only smoothness parameter available in this implementation. The higher it is, the smoother the function will be.\r\nTweaking the other two parameters allows you to gain performance at the price of a small precision loss. The default values are usually good.\r\n\r\nTo use the Pin-based normalization option, enter the number of blocks (e.g. array blocks, sub-arrays). The default value is 1 and when using this value each block will be normalized separately. The blocks are sorted in an ascending order and are grouped accordingly.\r\n\r\nThere is an option to exclude specific reporters in the calculation of correction factor. The excluded reporters will still be adjusted but not included in calculating the adjustment. The reporter ID's to be excluded are written on a single line separated by a '|' character (e.g. 1224|4563).\r\n\r\nFor more info on LOWESS:\r\nCleveland WS, Devlin SJ: Locally weighted regression: an approach to regression analysis by local fitting. J Am Stat Assoc 1988, 83:596-610.\r\n\r\nYang YH, Dudoit S, Luu P, Lin DM, Peng V, Ngai J, Speed TP: Normalization for cDNA microarray data: a robust composite method addressing single and multiple slide systematic variation. Nucleic Acids Res 2002, 30:e15. |
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execName run |
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geneAverages 0 |
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serialFormat 1 |
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url |
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minChannels 2 |
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maxChannels 0 |
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leaveStdin 0 |
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leaveStdout 0 |
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estimatedTime 3600 |
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defaultMaxRam 134217728 |
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usedColumns position\treporter\treporterId |
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usedFields l2ratio1_2\tl10intgmean1_2\tblock |
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columns position valueType name commonName options defaultValue enumOptions removed |
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20 |
% |
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1 h section section settings 0 |
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2 f fit_fraction Window size (fraction of points) 5 0.33 0 |
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3 f min_x_step Minimum log(intensity) step 5 0.1 0 |
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4 i n_iter Iterations 5 4 0 |
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5 i block_group_size Number of blocks in group 5 1 0 |
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6 e mode Adjust which reporters to use when calculating lowess Adjust which reporters to use when calculating lowess all all\tUse all\texclude\tExclude the following reporters\tinclude\tInclude the following reporters 0 |
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7 a reporters Repoterid's to include/exclude from the lowess calculation 20,80 0 |
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28 |
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