The Functional Analysis panel offers three alternatives for gene set overrepresentation analysis, relying on topGO [75], goseq [76], or the goana() function in the limma package [7]; users can perform the enrichment tests on genes that are significantly differentially regulated, either split by...
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exp.RMA<-exprs(exprsSet.RMA)##...
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...
Finally, if a visual comparison of the overlap in identified potential off-target sites between different nucleases or treatment conditions is desired, a Venn diagram of peak overlap in up to five different datasets can be plotted through the integrated limma package [50]. More detailed information...
The raw data must be provided as ExpressionSets in Bioconductor by means of manufacturer specific packages e.g. "affy" [27], "lumi" [28] or "limma" [29]. The "annotation" slot of the ExpressionSet must contain the name of a Bioconductor compliant annotation package. This should be checke...
Afterward, we perform a differential expression analysis (Additional file 3: Table S4 A, Fig. 4c). This involves normalizing counts with edgeR [8], forming a design matrix of interest, and controlling for heteroscedasticity in counts with voom [53]. limma [30] is used to construct...
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 ...