Hi, 

I have two questions about EdgeR pipeline. I am dealing with no replicate situation and have two conditions to check the differential expression. I am trying to apply GLM model for the analysis. I am bit confused about the design. 

I am running following commands to setup design - 

design <- model.matrix(~group, data=cds$samples)
design
 (Intercept) groupRest
Rest           1         1
Bcyt           1         0
attr(,"assign")
[1] 0 1
attr(,"contrasts")
attr(,"contrasts")$group
[1] "contr.treatment"

Is this design right for the experiment? how to set up to proper design for the experiment?

2) with this setup I carried out glm analysis. but the end I am not able to export my results in to the table. I run following command for exporting data -

write.table(lrt,file="EdgeR_all.txt",sep="\t",quote=F)

After this I am getting following error -

Error in data.frame(coefficients = c(-0.55319099962599, -0.597451121359484,  : 
  arguments imply differing number of rows: 25299, 1, 2

Please help me to solve this problem

Thank you in advance

Your design looks fine; dropping the second coefficient will give you DE between your two libraries. Obviously, there will be issues when you don't have any replicates. Read the advice in Section 2.10 of the user's guide, if you haven't already. On the other matter, if you want to save results, save the output of topTags instead:

save.me <- topTags(lrt, n=Inf, sort.by="none")
write.table(save.tags, file="EdgeR_all.txt", sep="\t", quote=FALSE)

Considering that you only have two samples, why do you even bother with a design matrix? Why not simply:

out <- exactTest(cds, dispersion=0.05)
topTags(out)

That will automatically find genes that are DE between the two groups as set in cds$samples$group.