Hi,

We are performing a study of 8 individuals with cancer. We have 8 pairs of
samples. Each pair consists of two samples from the same individual: one
from cancerous tissue and one from normal tissue.

We have used DESeq to perform a pooled comparison between the normal and
cancerous samples and find a number of genes that are differentially
expressed.

We would also like to perform a paired analysis (simple comparison between
the two tissue samples from the same individual). Our logic is that the
pooled analysis will tend to identify genes as differentially expressed only
if they are fairly consistently up or down-regulated across individuals.
But, the etiology of the same cancer type may be heterogeneous and we aim to
investigate this by performing the paired analysis. In connection with this,
I have two questions:
1. we read in the DESeq paper that this can be done, but are we correct in
believing that we can interpret the results as I describe above?
2. Does it make sense to do a paired analysis as described above or would it
make more sense to pool the normal tissues and then compare each cancerous
tissue to the pool?

Thanks for your help.

-- 
Tim :)

	[[alternative HTML version deleted]]

