These three data.frames contain data for the custom-made 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 peCC column holds the pairs' Pearson correlation coefficient calculated
on their expression intensities in the Tissue dataset (data originally from AtgenExpress Project).
CustomsTissue is data.frame that contains all custom-made CDF's probe set pairs
with Q75 >= 55.
CustomsTissueMC holds a subset of the pairs in CustomsTissue, namely those
whose metacorrelation coefficient is not NA are included.
For CustomsTissue.noBl, the pairs of CustomsTissue that align to each
other with BLAST in at least one direction with an E-value smaller than
10^{-10} were omitted.
Casneuf, Van de Peer and Huber,
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.
See Also
AffysTissue
Examples
data(CustomsTissue)
data(CustomsTissueMC)
data(CustomsTissue.noBl)
## see also the vignette
Results
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> library(XhybCasneuf)
Loading required package: affy
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from 'package:stats':
IQR, mad, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
rbind, rownames, sapply, setdiff, sort, table, tapply, union,
unique, unsplit
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Loading required package: ath1121501cdf
Loading required package: tinesath1cdf
Attaching package: 'tinesath1cdf'
The following objects are masked from 'package:ath1121501cdf':
i2xy, xy2i
Loading required package: RColorBrewer
Loading required package: grid
Warning messages:
1: replacing previous import 'AnnotationDbi::tail' by 'utils::tail' when loading 'ath1121501cdf'
2: replacing previous import 'AnnotationDbi::head' by 'utils::head' when loading 'ath1121501cdf'
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/XhybCasneuf/CustomsTissue.Rd_%03d_medium.png", width=480, height=480)
> ### Name: CustomsTissue
> ### Title: Custom-made CDF's probe set pairs
> ### Aliases: CustomsTissue CustomsTissueMC CustomsTissue.noBl
> ### Keywords: datasets
>
> ### ** Examples
>
> data(CustomsTissue)
> data(CustomsTissueMC)
> data(CustomsTissue.noBl)
>
> ## see also the vignette
>
>
>
>
>
> dev.off()
null device
1
>