matchprobes

[…] probesets to the latest genomic knowledge. For example Gautier et al have reannotated the Affymetrix HG-U133A probesets by mapping the probes against Human Refseq mRNA using the BioConductor package matchprobes [,]. Most reannotation efforts addressing GeneChip microarrays have remapped probes, or target sequences to external public databases of expressed sequence. One exception to this approach […]

[…] ould include more than 3 probes (see Additional File for further details). The remapped probe set definition was transformed into new probe sequence and CDF packages using the Bioconductor packages, matchprobes [] and makecdfenv []. R libraries of the probe and CDF packages, and annotation of the remapped probe sets are provided in Additional File . The probe remapping protocol is implemented in […]

[…] From existing raw expression files expression data were generated using a gene-centric CDF file. We applied RMA and quantile normalization and the matchprobes package in the Bioconductor framework to create one single data set. Only patients with pathologic stage I/II disease and less than 80 years old at diagnosis had their tumor’s expression p […]

[…] e probes to mRNA sequences with BLAT, which uses heuristics to speed up the search. To evaluate the accuracy of the BLAT search, we aligned the probes of the HG-U133A array also with the Bioconductor matchprobes package, which is based on exact string matching methods. The results obtained with BLAT and matchprobes were virtually the same (BLAT missed 52 of the 241 898 unique probes). The most ess […]