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Summarization
Each phylotype is targeted by multiple oligos on H/M/PITChip. The probe-level information is summarized to obtain the final abundancy estimates for the phylotypes. Various summaries are available in the ouput:
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sum Default option. Phylotype abundance is calculated as a sum of the matching oligos. Cross-hybridizing oligos that target multiple phylotypes are downweighted by the number of targets.
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rpa Robust Probabilistic Averaging method quantifies oligo-specific noise and downweights more noisy oligos. Oligos with multiple targets are also downweighted automatically.
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nmf Non-negative matrix factorization. Removes cross-hybridization effects based on oligo-phylotype mappings. Works on genus- and phylum levels (levels L1-L2).
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ave Average of the oligos. Does not take into account cross-hybridization of the oligos with multiple targets. Provided for backward compatibility; not recommended.