[BioC] RNAseq expression analysis using DESeq: technical replicates, paired samples

[Jinfeng Liu]

Hi All,

I'm trying to use DESeq for RNAseq expression analysis. I haven't been able to 

find information about how to deal with the following issues:

1) technical replicates
We have two biological samples, two libraries (of different insert size) were 

prepared for each of them. so I have four lanes of data in total and I want to 
do 

differential expression between the two samples. It doesn't look quite right to 

me to set up the condition vector as 

conds <- c( "Sample1", "Sample1","Sample2","Sample2") since they are only 

technical replicates, not biological. But I'm not sure what to do.

2) Paired samples
We have samples from three patients. For each patient, we have matched tumor and 

adjacent normal samples. How should we set up the analysis to capture the pair 

information?

Thanks a lot for your help.

Jinfeng