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Student's t-test

Source: R/analyze.R
analyze.t.Rd

Perform Student's t-tests on the data.

Usage

analyze.t(
  dataSet,
  ref = NULL,
  adjust.method = "none",
  paired = FALSE,
  pool.sd = FALSE
)

Arguments

dataSet

The 2d data set of data.

ref

A string (default = NULL) specifying the reference condition for comparison. If NULL, all pairwise comparisons are performed.

adjust.method

A string (default = "none") specifying the correction method for p-value adjustment:

  • "BH" or its alias "fdr": Benjamini and Hochberg (1995) .

  • "BY": Benjamini and Yekutieli (2001) .

  • "bonferroni": Bonferroni (1936) .

  • "hochberg": Hochberg (1988) .

  • "holm": Holm (1979) .

  • "hommel": Hommel (1988) .

  • "none": None

See p.adjust for more details.

paired

A boolean (default = FALSE) specifying whether or not to perform a paired test.

pool.sd

A boolean (default = FALSE) specifying whether or not to use a pooled standard deviation.

Value

A list comprising data frames for each comparison, with each data frame containing the means of the two compared conditions for each protein, the difference in means, and the p-values. Additionally, a separate data frame called "total" summarizes the results of multiple comparisons.

References

Benjamini Y, Hochberg Y (1995). “Controlling the False Discovery Rate: A Practical and Powerful Approach to Multiple Testing.” Journal of the Royal Statistical Society: Series B (Methodological), 57(1), 289–300. doi:10.1111/j.2517-6161.1995.tb02031.x .

Benjamini Y, Yekutieli D (2001). “The Control of the False Discovery Rate in Multiple Testing under Dependency.” The Annals of Statistics, 29(4), 1165–1188. doi:10.1214/aos/1013699998 .

Bonferroni CE (1936). “Teoria Statistica Delle Classi e Calcolo Delle Probabilità.” Pubblicazioni del R Istituto Superiore di Scienze Economiche e Commerciali di Firenze, 8, 3–62.

Hochberg Y (1988). “A Sharper Bonferroni Procedure for Multiple Tests of Significance.” Biometrika, 75(4), 800–802. doi:10.1093/biomet/75.4.800 .

Holm S (1979). “A Simple Sequentially Rejective Multiple Test Procedure.” Scandinavian Journal of Statistics, 6(2), 65–70. https://www.jstor.org/stable/4615733.

Hommel G (1988). “A Stagewise Rejective Multiple Test Procedure Based on a Modified Bonferroni Test.” Biometrika, 75(2), 383–386. doi:10.1093/biomet/75.2.383 .