[BioC] RNA-Seq fold change compared to control, without replicates

[Lisa Cohen]

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