[BioC] Paired comparisons in EdgeR

[Jussi Salmi]

Hello!


Thank you for the nice software and clear user guide. I am using EdgeR to analyse RNA-seq data. In the experiment there are several cell cultures with different knock-downs. The cell cultures are stimulated in two different ways. In the end, I want to compare the treated cultures to the untreated ones. The same untreated knock-down is compared to the same treated knock-down culture. I think that the study design produces paired comparisons because the same cultures are first used as the untreated ones and then they are treated and compared against the untreated.

I have come up with the following code, based on the user guide:

x<-read.delim("htseqout.edger", sep=" ",row.names="Symbol")
group<-factor(c(21,21,19,19,6,6,8,8,12,12,18,18,20,20,11,11,9,9,23...
y<-DGEList(counts=x,group=group)
design<-model.matrix(~0+group, data=y$samples)
colnames(design)<-levels(y$samples$group)
y<-estimateGLMTrendedDisp(y,design)
y<-estimateGLMTagwiseDisp(y,design)
fit<-glmFit(y,design)
?lrt0203<-glmLRT(fit,contrast=c(0,1,-1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0))
tt0203<-topTags(lrt0203, n=13000)
write.table(tt0203,file="tt0203")

[several other comparisons)

I tried to understand whether this is a good way to analyse paired samples or is there a better way?

Thanks,

Jussi Salmi
PhD computer Science
Centre for Biotechnology, Turku, Finland

> sessionInfo()
R version 3.1.0 (2014-04-10)
Platform: x86_64-pc-linux-gnu (64-bit)

locale:
 [1] LC_CTYPE=fi_FI.UTF-8       LC_NUMERIC=C               LC_TIME=fi_FI.UTF-8       
 [4] LC_COLLATE=fi_FI.UTF-8     LC_MONETARY=fi_FI.UTF-8    LC_MESSAGES=fi_FI.UTF-8   
 [7] LC_PAPER=fi_FI.UTF-8       LC_NAME=C                  LC_ADDRESS=C              
[10] LC_TELEPHONE=C             LC_MEASUREMENT=fi_FI.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] splines   stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] edgeR_3.4.2   limma_3.18.13

loaded via a namespace (and not attached):
[1] tools_3.1.0

-- 
Jussi Salmi, PhD
http://www.btk.fi/index.php?id=12&sort=&pid=282