Hi, I'm not sure how to get differential gene expression for whole genome arrays with XPS. In the manual, FIRMA was used to find differential alternative splicing for exon arrays. For gene expression, should I use limma? Thanks, Quynh

Dear Quynh, If you have only two groups, then you can use xps for differential expression, see vignette 'xps.pdf' Chapters 6.1 and 6.2, and example code in 'xps/examples/script4exon.R' (4.step). If you have more than two groups, you need to use limma, which most people prefer anyhow. In this case see 'xps.pdf' Appendix A.3 how to create a class 'ExpressionSet' for use with limma. Best regards, Christian On 7/28/14 8:05 AM, Quynh Tran wrote: > Hi, > > I'm not sure how to get differential gene expression for whole genome arrays with XPS. In the manual, FIRMA was used to find differential alternative splicing for exon arrays. For gene expression, should I use limma? > > Thanks, > Quynh > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >