matchBoxExpression: Example data: ranking from three differential gene expression...

In marchion/matchBox: Utilities to compute, compare, and plot the agreement between ordered vectors of features (ie. distinct genomic experiments). The package includes Correspondence-At-the-TOP (CAT) analysis.

Description

List of differentially expressed genes from three distinct experiments from which the identifiers and the ranking statistics to be used for computing overlap proportions will be retrieved. This type of object is the starting point of a CAT-plot analysis,

Usage

data(matchBoxExpression)

Format

This object is a list of data.frames containing at least two common columns, one for the identifiers and one for the ranking statistics. The common columns must have the same column names. In the provided example the following columns are present in each data.frame:

SYMBOL: Gene symbol column;

GENENAME: Gene name column;

ENTREZID: ENTREZ Gene identifier column;

logFC: Log2 fold-change column;

AveExpr: Average expression (A-value) column;

t: moderated t-statistics column;

P.Value: P-value column;

adj.P.Val: adjusted P-value column;

B: B-statitics (log-odds) column;

The statistics were computed using the topTable function from limma.

Author(s)

Luigi Marchionni [e-mail]

References

Irizarry, R. A.; Warren, D.; Spencer, F.; Kim, I. F.; Biswal, S.; Frank, B. C.; Gabrielson, E.; Garcia, J. G. N.; Geoghegan, J.; Germino, G.; Griffin, C.; Hilmer, S. C.; Hoffman, E.; Jedlicka, A. E.; Kawasaki, E.; Martinez-Murillo, F.; Morsberger, L.; Lee, H.; Petersen, D.; Quackenbush, J.; Scott, A.; Wilson, M.; Yang, Y.; Ye, S. Q. and Yu, W. Multiple-laboratory comparison of microarray platforms. Nat Methods, 2005, 2, 345-350

Ross, A. E.; Marchionni, L.; Vuica-Ross, M.; Cheadle, C.; Fan, J.; Berman, D. M.; and Schaeffer E. M. Gene Expression Pathways of High Grade Localized Prostate Cancer. Prostate 2011, 71, 1568-1578

Benassi, B.; Flavin, R.; Marchionni, L.; Zanata, S.; Pan, Y.; Chowdhury, D.; Marani, M.; Strano, S.; Muti, P.; and Blandino, G. c-Myc is activated via USP2a-mediated modulation of microRNAs in prostate cancer. Cancer Discovery, 2012, March, 2, 236-247

marchion/matchBox documentation built on May 9, 2019, 4:07 p.m.