[BioC] XPS differential expression

[cstrato]

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
>