举个从GEO数据库下载的样例,逐步介绍RMA进行CEL表达谱数据标准化,以及limma算法提取差异表达基因的过程。 source("链接") biocLite("affy") biocLite("Biobase") biocLite("tkWidgets") library(affy) AffyData<-ReadAffy(widget=TRUE) exprsSet.RMA<-rma(AffyData)##用rma方法处理数据 ...
Chromatin immunoprecipitation (ChIP) followed by high-throughput sequencing (ChIP-seq) or ChIP followed by genome tiling array analysis (ChIP-chip) have become standard technologies for genome-wide identification of DNA-binding protein target sites. A nu
limma powers differential expression analyses for RNA-sequencing and microarray studies. Nucleic Acids Res. 2015;43(7):e47. 21. Himes BE, Jiang X, Wagner P, Hu R, Wang Q, Klanderman B, Whitaker RM, Duan Q, Lasky-Su J, Nikolos C, Jester W, Johnson M, Panettieri Jr R, Tanti...
orhelp()at the R console. Some of these vignettes, such as theUser's Guide that accompanies thelimmapackage (pdf), include multiple case studies and carefully explain the statistical foundations of the methods implemented in the package. There is also a dedicatedsupport forumcontaining many years...
Afterward, we perform a differential expression analysis (Additional file3: Table S4 A, Fig.4c). This involves normalizing counts withedgeR[8], forming a design matrix of interest, and controlling for heteroscedasticity in counts withvoom[53].limma[30] is used to construct a linear model of ...
these tracks can be a daunting task, particularly if there are a large number of binding sites or the binding sites are distributed widely across the genome. Results: We have developed ChIPpeakAnno as a Bioconductor package within the statistical programming ...