| Title: | MEEBO set and MEEBO controls. |
|---|---|
| Description: | R objects describing the MEEBO set. |
| Authors: | Agnes Paquet |
| Maintainer: | Agnes Paquet <[email protected]> |
| License: | LGPL |
| Version: | 1.51.0 |
| Built: | 2026-10-10 10:27:26 UTC |
| Source: | https://github.com/bioc/MEEBOdata |
MEEBOset: character matrix containing annotations for all oligos in the MEEBO set, e.g. sequence id, name, description of the oligo. The annotations used here come from the original MEEBO dataset and are not updated.
MEEBOctrl: list of matrices describing mismatch transcripts and negative controls. For each of the 10 unique transcripts used to design the mismatch controls, we provide some annotations for all derived mismatch probes (like sequnce id, array identifier, description...), the type of mismatch (anchored or Distributed), the number of mismatched bases, and the binding energy. The last object is a list of negative controls identifiers.
MEEBOtilingres: list of 11 vectors, one for each sequence used to design the series of tiling controls. Each vector contains the unique MEEBO identifiers and the distance from 3' end for each tiling controls recognizing this sequence.
These data were derived from the MEEBO set description files provided by Ash Alizadeh. The R code used to parse the file is available upon request. For more information about the MEEBO set, please refer to http://alizadehlab.stanford.edu.
RDI108\_n.gpr is an example of hybridization on MEEBO arrays, using a doping-control mixture from SFGF.
StanfordDCV1.7complete.txt is an example of spike-type file from SFGF.
These data were provided by members of the Brown lab (Stanford) and the Stanford Shared Genomics Core Facility.