使用R/Bioconductor对Affytron Exon 1.0 ST阵列进行可重现探针水平分析
Reproducible probe-level analysis of the Affymetrix Exon 1.0 ST array with R/Bioconductor
摘要：
跨样品的基因的不同转录物的存在可以通过全转录组微阵列来分析。由于大量的数据和在进行实际分析之前采用的各种各样的预处理和过滤步骤，从已发表的微阵列数据再现结果是一个挑战。为了保证方法学发展的坚实基础，将新方法的结果与以前的结果进行比较，确保所有分析对其他研究人员来说是完全可重复的至关重要。我们在这里给出了一个详细的工作流程，关于如何在R/Bioconductor中仅在探针和概率水平上对GeneChip Human Exon 1.0 ST Array进行可重复的分析，并根据其易用性选择软件包。为了验证所提出的工作流程的使用，我们使用各种统计方法分析了公开数据集中的差异剪接和差异基因表达。我们相信这项研究将为其他研究人员提供一种在不同注释水平上访问基因表达数据的简单方法，并提供开发自己的工具以用于GeneChip Human Exon 1.0 ST Array的可重复分析所需的足够细节。
英文摘要：
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 due to the vast amounts of data and the large variety of pre-processing and filtering steps employed 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 proposed workflow we analyse differential splicing and differential gene expression in a publicly available dataset using various statistical methods. We believe this study will provide other researchers with an easy way of accessing gene expression data at different annotation levels and with the sufficient details needed for developing their own tools for reproducible analysis of the GeneChip Human Exon 1.0 ST Array.
机构、总结、中文摘要均由AI分析而来，可能存在错误，请以论文正文为准。
