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Indeed it is possible that such an effect is removed by the normalization routine that we use.
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The script offers several options, allowing choice between absorption conversion methods (line or image), thresholding values for these methods, and parameters to be passed to the normalization routine.
The spectra were processed with the Perkin Elmer Spectrum software and normalized with the implemented normalization routine.
The old up-by-the-bootstraps routine.
Then, by applying a weighted normalization routine to these consecutive values, an implicit stabilizer is formed: (19).
The SCB is related to other scoring-table statistics by different normalization routines.
Ratio values were normalized using the print-tip Loess normalization routine [70] and a linear model fitted to determine a final expression value for each mRNA [71].
Significantly regulated biological pathways were identified using a modified version of the sigPathway algorithm [ 16] incorporating a modified normalization routine and using gene sets collections C1 to C5 defined by the Molecular Signatures Database (MSigDB) [ 17].
Low flash-to-flash intensity variation is important, as the system does not yet have an intensity normalization routine.
The final normalization factor was obtained by dividing the normalization ratio of each stage by the normalization ratio of the ring stage.
The p-value is not altered by the normalization.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com