Hi I am a novice for RNA Seq data analysis, and I am trying to compare groups which belong to more than 2 groups. I am unsure whether I have to specify this in 'DGEList' function or the 'exactTest' function, and how exactly to specify this? For example it may have 3 categories : Tumour_typeA, Normal, Tumour_typeB with each sample belonging to 1 of these. If I now want to find differentially expressed genes between Tumour_typeA and Tumour_typeB (and skip the 'Normals' ), where can I specify this. Any advice or help you can provide will be very helpful. Thanks Sakshi Sakshi Gulati PhD Student Biomolecular Modelling Laboratory Cancer Research UK London Research Institute 44 Lincoln's Inn Fields London WC2A 3LY NOTICE AND DISCLAIMER This e-mail (including any attachments) is intended for ...{{dropped:19}}

Hi Saskhi, These are pretty straightforward analyses and you have at least 2 ways for this particular comparison: 1. Use "classic" edgeR and specify the groups you want to make comparisons between using the 'pair' argument of the exactTest() function. 2. Use "GLM" edgeR and define an appropriate contrast for your difference of interest. They should, in fact, be very similar. There are various examples in the user's guide: http://www.bioconductor.org/packages/release/bioc/vignettes/edgeR/inst /doc/edgeRUsersGuide.pdf Best, Mark On 07.11.2012, at 12:57, Sakshi Gulati wrote: > Hi > > I am a novice for RNA Seq data analysis, and I am trying to compare groups which belong to more than 2 groups. I am unsure whether I have to specify this in 'DGEList' function or the 'exactTest' function, and how exactly to specify this? > For example it may have 3 categories : Tumour_typeA, Normal, Tumour_typeB with each sample belonging to 1 of these. If I now want to find differentially expressed genes between Tumour_typeA and Tumour_typeB (and skip the 'Normals' ), where can I specify this. > > Any advice or help you can provide will be very helpful. > > > > Thanks > > Sakshi > > > Sakshi Gulati > PhD Student > Biomolecular Modelling Laboratory > Cancer Research UK London Research Institute > 44 Lincoln's Inn Fields > London WC2A 3LY > > > NOTICE AND DISCLAIMER > This e-mail (including any attachments) is intended for ...{{dropped:19}} > > _______________________________________________ > 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