Mercurial > repos > galaxyp > cardinal_preprocessing
changeset 12:e0669b1854b1 draft
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit ca7bdf2cbc8a79278c56ab6890e038710a2a9ad8"
| author | galaxyp |
|---|---|
| date | Thu, 22 Oct 2020 20:38:29 +0000 |
| parents | e86a8be551b9 |
| children | 6b36be80febb |
| files | preprocessing.xml |
| diffstat | 1 files changed, 6 insertions(+), 4 deletions(-) [+] |
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--- a/preprocessing.xml Tue Oct 06 08:12:49 2020 +0000 +++ b/preprocessing.xml Thu Oct 22 20:38:29 2020 +0000 @@ -836,15 +836,17 @@ **Options** -- Normalization: Normalization of intensities to total ion current (TIC) or to root-mean-square (RMS) -- Baseline reduction: Baseline reduction removes background intensity generated by chemical noise (common in MALDI datasets) +- Normalization: normalization of intensities to total ion current (TIC) or to root-mean-square (RMS) +- Baseline reduction: baseline reduction removes background intensity generated by chemical noise (common in MALDI datasets) - Smoothing: Smoothing of the peaks reduces noise and improves peak detection +- m/z alignment: removes small m/z shifts between spectra - Peak picking: relevant peaks are picked while noise-peaks are removed (needs peak alignment afterwards) - Peak alignment: only possible after peak picking, m/z inaccuracies are removed by alignment of same peaks to a common m/z value; if no reference is given the peaks are aligned to the local maxima of the mean spectrum of the current dataset; external reference data can be used from another MSI data file or a tabular file with m/z values, but then only the m/z from the reference will be kept - Peak filtering: removes peaks that occur only in a small proportion of pixels. If not sure which cut off to choose run quality control tool first and decide according to the number of peaks per m/z plot -- Peak binning: extracts peaks intensities (from a profile dataset) for a list of m/z (reference) values -- Data reduction: binning or resampling to reduce data +- Peak binning: extracts peaks intensities, either peak height or area under curve (from a profile dataset) for a list of m/z (reference) values +- m/z binning: generates new m/z bins - Transformation: log2 or squareroot transformation of all intensities; when using log2 transformation zero intensities will become NA, this can lead to compatibility problems. + **Output**