R: Example data: ranking from three differential gene expression...
matchBoxExpression
R Documentation
Example data: ranking from three differential gene expression experiments
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.
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