Continuous Analysis BrainArray: Submission Release

This is a sample repository showing a Continuous Analysis Workflow (https://github.com/greenelab/continuous_analysis) for RNA-Seq analysis. A description of continuous analysis is available as a pre-print: http://dx.doi.org/10.1101/056473

In this example we evaluate the effect of different custom chip description files (CustomCDF). To evaluate the impact of differing CDF versions, we downloaded a recently published public gene expression dataset. This experiment examined differential expression between normal HeLa cells and HeLa cells with TIA1 and TIAR knocked down (GEO Series Ascension number GSE47664). We performed a parallel analysis using each of the three versions that we found installed on machines that we could access (18, 19, and 20). Each version identifies a different number of significantly altered genes, demonstrating the challenge of reproducible analysis.