An environment with probe mapping information for the Scerevisiae tiling array

Description

The environment contains probe mapping information for the Affymetrix Scerevisiaetiling chip from 2004, which was custom-made for the Stanford Genome Center. The chips tile the complete genome of S. cerevisiae in steps of 8 bases, separately for each strand of each chromosome. The two tiles for one chromosome (Watson and Crick strands) are offset by 4 bases.

In the following a brief description of the 138 elements of the probeAnno environment.

probeReverse: a list of 8 factors, each of length 6553600, corresponding to the rows of davidTiling. For example, if the probe corresponding to the j-th row in davidTiling maps to the coding sequence of a gene, then the factor level of probeRevers$CDS[j] is the name of the gene, and the empty string "" otherwise. This applies to samples that were hybridized to the chip after a reverse transcription step.

probeDirect: analogous to probeReverse, but for samples that were hybridized to the chip without a reverse transcription step. The probes map to the opposite chromosomal strand compared to experiments with reverse transcription.

1.+.index: indices (from 1...6553600, corresponding to the rows of davidTiling) of probes mapping to the Watson strand of chromosome 1.

1.+.start, 1.+.end: start and end positions in genomic coordinates of the alignments of the probes (in the same order as in 1.+.index) to the Watson strand of chromosome 1. For 25-mers, the values in 1.+.end are those in 1.+.start plus 24, but not all probes on the array are 25-mers.

1.-.unique: specificity of the probe:

0

has exactly one perfect match (PM) and no near-matches in the genome

1

has exactly one PM and some near-matches

2

has no PM but one or more near-matches

3

has multiple PMs in the genome

1.-.index, 1.-.start, 1.-.end, 1.-.unique: analogous to the above, but for the Crick strand of chromosome 1. 2.+.index, 2.+.start, 2.+.end, 2.-.unique: analogous to the above, but for the Watson strand of chromosome 2; and so forth. "Chromosome 17" is mitochondrial DNA.

Usage

data("probeAnno")

Author(s)

W. Huber huber@ebi.ac.uk

Source

Probe sequences were obtained from Affymetrix in a file called S.cerevisiae_tiling.1lq. The genomic sequences of the S. cerevisiae chromosomes were downloaded from ftp://genome-ftp.stanford.edu/pub/yeast/data_download/sequence/genomic_sequence/chromosomes/fasta on 7 Aug 2005, 18:16 BST in 17 files chr01.fsa–chr16.fsa, and chrmt.fsa. The probe sequences were matched against the chromosomal sequencences with the program MUMmer, see the script mapProbesToGenome.sh (in the inst/scripts directory of this package). MUMmer results were parsed and processed into the probeAnno environment with the script makeProbeAnno.R (in the inst/scripts directory of this package).

Examples

data("probeAnno")
ls(probeAnno)
str(probeAnno$"1.+.start")