Reproducible probe-level analysis of the Affymetrix Exon 1.0 ST array with R/Bioconductor.

ABSTRACT: The presence of different transcripts of a gene across samples can be analysed by whole-transcriptome microarrays. Reproducing results from published microarray data represents a challenge owing to the vast amounts of data and the large variety of preprocessing and filtering steps used before the actual analysis is carried out. To guarantee a firm basis for methodological development where results with new methods are compared with previous results, it is crucial to ensure that all analyses are completely reproducible for other researchers. We here give a detailed workflow on how to perform reproducible analysis of the GeneChip®Human Exon 1.0 ST Array at probe and probeset level solely in R/Bioconductor, choosing packages based on their simplicity of use. To exemplify the use of the propos

SUBMITTER: Rodrigo-Domingo M 

PROVIDER: S-EPMC4103539 | biostudies-literature | 2014 Jul

REPOSITORIES: biostudies-literature