AffysTissue {XhybCasneuf} | R Documentation |
Affymetrix' CDF probe set pairs
data(AffysTissue) data(AffysTissueMC) data(AffysTissue.noBl)
These three data.frames contain data for Affymetrix' CDF's probe set pairs with Q75 >= 55.
The pr
and target
columns hold the names of probe set X and Y, respectively.
Column alSum
contains the Q75 value of the alignment scores of X's
reporters to the transcript of Y.
The meant2hit
and PSofTarget
columns contain respectively the gene locus
the probe set was designed to target and the probe set ID of the off-target Y,
according to Affymetrix (extracted from ATH1-121501_annot.csv).
The peCC
column holds the pairs' Pearson correlation coefficient calculated
on their expression intensities in the Tissue dataset (data originally from AtgenExpress Project).
AffysTissue
is data.frame that contains all Affymetrix' CDF's probe set pairs
with Q75 >= 55.
AffysTissueMC
holds a subset of the pairs in AffysTissue
, namely those
whose metacorrelation coefficient is not NA are included.
For AffysTissue.noBl
, the pairs of AffysTissue
that align to each
other with BLAST in at least one direction with an E-value smaller than 10^{-10}
were omitted.
Tineke Casneuf tine@ebi.ac.uk
Casneuf, Van de Peer and Huber (Submitted); AtgenExpress data used: Schmid, M., Davison, T. S., Henz, S. R., Pape, U. J., Demar, M., Vingron, M. Schoelkopf, B. Weigel, D., and Lohmann, J. (2005) A gene expression map of Arabidopsis development. Nature Genetics, 37, 501-506.
data(AffysTissue) data(AffysTissueMC) data(AffysTissue.noBl) ## see also the vignette