Sample-matched RNA-Seq gene expression analysis

Question

[Nicolas Rosewick]

HI,

I've a bunch of sample-matched (T0 and T1) data of uninfected and infected (virus) RNA-Seq samples. So:

                T0      T1                
Patient 1       0.4%    40%
Patient 2       0.5%    60%
Patient 3       0.2%    35%

where the percentage represent the percentage of cells infected by the virus. In order to detect differentially expressed genes (DEGs) induced/repressed by the presence of the virus, how can I take into account the percentage of infected cells that varies between patient ? In general, I use DESeq for this type of analysis but I don't know how to take into account the percentage of infected cells.

Thanks

[Devon Ryan]

I assume that your current model is something of the form ~patient + time. Have you considered changing that up to ~patient + infected_percentage? That would be my gut reaction of one method. You might also logit transform those percentages, though I really don't have a good feeling about how useful that would be. I guess in general the question become how variable the percentage is (both in T0 and T1) and how much that correlates with expression changes (presumably a PCA plot or heatmap would be helpful here).

[Nicolas Rosewick]

the problem is that I don't know which gene is targeted by the virus (the aim of the analysis in fact), so it will be difficult to correlate percentage and expression changes..

[Devon Ryan]

Right, but using a PCA plot or something like that would be useful. You don't need to know the DE genes beforehand for that.