Output class of NOISeq

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Description

Output object containing the results from differential expression analysis by noiseq or noiseqbio.

Slots/List Components

Objects of this class contain (at least) the following list components:

comparison: String indicating the two experimental conditions being compared and the sense of the comparison.

factor: String indicating the factor chosen to compute the differential expression.

k: Value to replace zeroes in orden to avoid inderminations when computing logarithms.

lc: Correction factor for length normalization. Counts are divided by length^lc.

method: Normalization method chosen. It can be one of "rpkm" (default), "uqua" (Upper Quartile), "tmm" (Trimmed Mean of M) or "n" (no normalization).

replicates: Type of replicates: "technical" for technical replicates and "biological" for biological ones.

results: R data frame containing the differential expression results, where each row corresponds to a feature. The columns are: Expression values for each condition to be used by noiseq or noiseqbio (the columns names are the levels of the factor); differential expression statistics (columns "M" and "D" for noiseq or "theta" for noiseqbio); probability of differential expression ("prob"); "ranking", which is a summary statistic of "M" and "D" values equal to -sign(M)*sqrt(M^2 + D^2), than can be used for instance in gene set enrichment analysis (only when noiseq is used); "length" and "GC" of each feature (if provided); chromosome where the feature is ("Chrom"), if provided; start and end position of the feature within the chromosome ("GeneStart", "GeneEnd"), if provided.

nss: Number of samples to be simulated for each condition (only when there are not replicates available).

pnr: Percentage of the total sequencing depth to be used in each simulated replicate (only when there are not replicates available). If, for instance, pnr = 0.2 , each simulated replicate will have 20% of the total reads of the only available replicate in that condition.

v: Variability of the size of each simulated replicate (only used by NOISeq-sim).

Methods

This class has an specific show method in order to work and print a summary of the elements which are contained.

Author(s)

Sonia Tarazona