Hi all, I have been analysing some RNA-seq data using the packages DEGseq, edgeR and baySeq and I was wondering if anyone could help me to be able to produce a plot to show the number of DE found using these packages at an FDR of 0.1%. or possibly direct me to any good source that can be used to achieve this. I will certainly appreciate any help. Kind Regards Tina

Hi Tina, Limma has some functions related to plotting Venn diagrams, is what you're looking for? For example: > a = runif(100) > b = runif(100) > library(limma) > comparison <- data.frame(de.a=a <= 0.1, de.b=b <= 0.1) > head(comparison) de.a de.b 1 FALSE TRUE 2 FALSE TRUE 3 FALSE FALSE 4 FALSE FALSE 5 FALSE TRUE 6 FALSE FALSE > table(comparison) de.b de.a FALSE TRUE FALSE 79 12 TRUE 9 0 > vc <- vennCounts(comparison) > vennDiagram(vc) Also, there are alternative methods at this resource: http://manuals.bioinformatics.ucr.edu/home/ht-seq hope this helps, Vince On Thu, Mar 1, 2012 at 5:50 PM, Tina Asante Boahene <ma08tta@brunel.ac.uk>wrote: > Hi all, > > I have been analysing some RNA-seq data using the packages DEGseq, edgeR > and baySeq and I was wondering if anyone could help me to be able > to produce a plot to show the number of DE found using these packages at > an FDR of 0.1%. or possibly direct me to any good source that can be used > to achieve this. > > I will certainly appreciate any help. > > > Kind Regards > > Tina > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > -- Vince Buffalo Statistical Programmer Bioinformatics Core UC Davis Genome Center University of California, Davis "There's real poetry in the real world. Science is the poetry of reality." -Richard Dawkins [[alternative HTML version deleted]]

Hi Tina On 03/02/2012 02:50 AM, Tina Asante Boahene wrote: > I have been analysing some RNA-seq data using the packages DEGseq, edgeR and baySeq and I was wondering if anyone could help me to be able > to produce a plot to show the number of DE found using these packages at an FDR of 0.1%. or possibly direct me to any good source that can be used to achieve this. Not answering your question, but: An FDR of 0.1% (i.e., 0.001)? This is absurdly small. Are you sure you have proper replication? Simon

Hi all, I have been analysing some RNA-seq data using the packages DEGseq, edgeR and baySeq and I was wondering if anyone could help me to be able to produce a plot to show the number of DE found using these packages at an FDR of 1%. or possibly direct me to any good source that can be used to achieve this. I will certainly appreciate any help. Kind Regards Tina