Affymetrix' CDF probe set pairs

Description

Affymetrix' CDF probe set pairs

Usage

data(AffysTissue)
data(AffysTissueMC)
data(AffysTissue.noBl)

Format

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.

Author(s)

Tineke Casneuf tine@ebi.ac.uk

References

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

CustomsTissue

Examples

data(AffysTissue)
data(AffysTissueMC)
data(AffysTissue.noBl)

## see also the vignette

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
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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/AffysTissue.Rd_%03d_medium.png", width=480, height=480)
> ### Name: AffysTissue
> ### Title: Affymetrix' CDF probe set pairs
> ### Aliases: AffysTissue AffysTissueMC AffysTissue.noBl
> ### Keywords: datasets
> 
> ### ** Examples
> 
> data(AffysTissue)
> data(AffysTissueMC)
> data(AffysTissue.noBl)
> 
> ## see also the vignette
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>