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FASDA-NORMALIZE(1) General Commands Manual FASDA-NORMALIZE(1) NAME fasda normalize - Normalize abundances given raw counts and lengths SYNOPSIS fasda normalize abundance1.tsv abundance2.tsv ... OPTIONS --mrn Use Mean Ratios Normalization [default] DESCRIPTION The fasda normalize command attempts to normalize the read counts in 2 or more kallisto-style abundance.tsv files. Each TSV file represents a biological sample. Multiple samples are required in order to statisti- cally estimate the normalization factor. Currently, only Median Ratios Normalization (MRN) is implemented. This method computes the average count for all samples of a given feature (e.g. gene or transcript), then the ratio of each count to the average for the feature, and finally the median ratio for each sample. The me- dian ratio is the scaling factor for that sample. This should, in the- ory, normalize for differences in library size (total reads for a given sample). This method assumes that technical effects are the same for DE and non-DE genes and that expression is roughly symmetric (there are equal numbers of up-regulated and down-regulated genes). [Evans, et al, 2018 doi: 10.1093/bib/bbx008] Additional normalization methods, including the use of spike-in con- trols, are planned for the future. FILES abundance.tsv - kallisto-style abundance estimates SEE ALSO fasda-abundance(1), fasda-fold-change(1) BUGS Please report bugs to the author and send patches in unified diff for- mat. (man diff for more information) AUTHOR J. Bacon FASDA-NORMALIZE(1)
NAME | SYNOPSIS | OPTIONS | DESCRIPTION | FILES | SEE ALSO | BUGS | AUTHOR
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