csSAM: csSAM

In csSAM: csSAM - cell-specific Significance Analysis of Microarrays

Description

Computes the constrast between groups for the deconvolved cell-specific expression for each cell-type

Usage

  csSAM(ghat1, se1, n1, ghat2, se2, n2, standardize,
    medianCenter = TRUE, nonNeg = FALSE)

Arguments

ghat1	Expression matrix of deconvolved cell-specific gene expression estimates for group 1.
se1	Standard error group 1
n1	Group 1 size
ghat2	Expression matrix of deconvolved cell-specific gene expression estimates for group 2.
se2	Standard error group 2
n2	Group 2 size
standardize	Standardize contrast values
medianCenter	Median center rhat distributions for each cell-type
nonNeg	Negative values not allowed such as in a single channel microarray. Zero them if negative (a conervative option)

Value

A matrix object with the result of contrasting the average cell-specific expression profile of the two groups, per cell-type (Size k by g where k is the number of cells and g is the number of genes).

Author(s)

Shai Shen-Orr, Rob Tibshirani, Narasimhan Balasubramanian, David Wang

References

Shen-Orr SS, Tibshirani R, Khatri P, Bodian DL, Staedtler F, Perry NM, Hastie T, Sarwal MM, Davis MM and Butte AJ (2010). "Cell type-specific gene expression differences in complex tissues." _Nature methods_, *7*(4), pp. 287-9. ISSN 1548-7105, <URL: http://dx.doi.org/10.1038/nmeth.1439>, <URL: http://www.ncbi.nlm.nih.gov/pubmed/20208531>.

csSAM documentation built on May 2, 2019, 5:52 a.m.