I am analyzing a set of RNA-Seq data without replicates, possibly using edgeR. (We understand limitations and are only interested in descriptive analyses.) There are three different treatments (OC, OD, UD) and one control (UC). For each treatment, I want to find transcripts with highest and lowest fold changes compared to the control. What is the best way to do this? Thank you, Lisa Cohen Output from what I have tried: >data<-read.csv("spongeRNASeq.csv") >reads<-data.frame(data[,c(14,25,36,47)]) >rownames(reads)<-data$Feature.ID > head(reads) OC...OC...Total.gene.reads gi|10039333|dbj|BAB13309.1| 878 gi|10039335|dbj|BAB13310.1| 694 gi|10045222|emb|CAC07820.1| 84 gi|100913263|gb|ABF69531.1| 15 gi|10121725|gb|AAG13342.1|AF266222_1 46 gi|1017427|emb|CAA62189.1| 142 UC...UC...Total.gene.reads gi|10039333|dbj|BAB13309.1| 1078 gi|10039335|dbj|BAB13310.1| 847 gi|10045222|emb|CAC07820.1| 91 gi|100913263|gb|ABF69531.1| 4 gi|10121725|gb|AAG13342.1|AF266222_1 108 gi|1017427|emb|CAA62189.1| 176 OD...OD...Total.gene.reads gi|10039333|dbj|BAB13309.1| 1241 gi|10039335|dbj|BAB13310.1| 983 gi|10045222|emb|CAC07820.1| 86 gi|100913263|gb|ABF69531.1| 13 gi|10121725|gb|AAG13342.1|AF266222_1 20 gi|1017427|emb|CAA62189.1| 189 UD...UD...Total.gene.reads gi|10039333|dbj|BAB13309.1| 1303 gi|10039335|dbj|BAB13310.1| 908 gi|10045222|emb|CAC07820.1| 97 gi|100913263|gb|ABF69531.1| 11 gi|10121725|gb|AAG13342.1|AF266222_1 25 gi|1017427|emb|CAA62189.1| 173 > dge<-DGEList(count=reads) >y<-cpm(dge,prior.count=2,log=TRUE) > head(y) OC...OC...Total.gene.reads gi|10039333|dbj|BAB13309.1| 5.63375891 gi|10039335|dbj|BAB13310.1| 5.29524053 gi|10045222|emb|CAC07820.1| 2.27509169 gi|100913263|gb|ABF69531.1| -0.07989017 gi|10121725|gb|AAG13342.1|AF266222_1 1.43064777 gi|1017427|emb|CAA62189.1| 3.02034770 UC...UC...Total.gene.reads gi|10039333|dbj|BAB13309.1| 5.831082 gi|10039335|dbj|BAB13310.1| 5.483847 gi|10045222|emb|CAC07820.1| 2.291848 gi|100913263|gb|ABF69531.1| -1.687601 gi|10121725|gb|AAG13342.1|AF266222_1 2.534316 gi|1017427|emb|CAA62189.1| 3.229247 OD...OD...Total.gene.reads gi|10039333|dbj|BAB13309.1| 5.89318821 gi|10039335|dbj|BAB13310.1| 5.55758268 gi|10045222|emb|CAC07820.1| 2.07426804 gi|100913263|gb|ABF69531.1| -0.47169802 gi|10121725|gb|AAG13342.1|AF266222_1 0.07832464 gi|1017427|emb|CAA62189.1| 3.19153484 UD...UD...Total.gene.reads gi|10039333|dbj|BAB13309.1| 5.8430837 gi|10039335|dbj|BAB13310.1| 5.3230991 gi|10045222|emb|CAC07820.1| 2.1261583 gi|100913263|gb|ABF69531.1| -0.7775835 gi|10121725|gb|AAG13342.1|AF266222_1 0.2618902 gi|1017427|emb|CAA62189.1| 2.9463446

Hi, On Tue, Dec 17, 2013 at 1:27 PM, Lisa Cohen <lisa.johnson.cohen at="" gmail.com=""> wrote: > I am analyzing a set of RNA-Seq data without replicates, possibly > using edgeR. (We understand limitations and are only interested in > descriptive analyses.) There are three different treatments (OC, OD, > UD) and one control (UC). > > For each treatment, I want to find transcripts with highest and lowest > fold changes compared to the control. What is the best way to do this? Have you read through the user's guide that comes with edgeR? http://bioconductor.org/packages/release/bioc/vignettes/edgeR/inst/doc /edgeRUsersGuide.pdf There's lots of very useful stuff to be learned there w.r.t analyses of RNA-seq data, so you should definitely do so. There is even a section entitled "What do do if you have no replicates." If you still have questions after you've read through that guide, then please post with specific questions regarding particular steps of the analysis you are having trouble with. If you are new to these types of analyses, reading through the user guides that come with limma and DESeq2 will be very informative as well, and highly recommended. HTH, -steve -- Steve Lianoglou Computational Biologist Genentech

GFold is a method that was created for this. You can read about it http://www.tongji.edu.cn/~zhanglab/GFOLD/index.html There is no R implementation. You will need to use a command line interface. -------------------------------------- Dario Strbenac PhD Student University of Sydney Camperdown NSW 2050 Australia