AffysTissue {XhybCasneuf} | R Documentation

## 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 (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.

### See Also

`CustomsTissue`

### Examples

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

    ## see also the vignette

[Package XhybCasneuf version 1.0.0 Index]