Hi,

I have some doubts about my data.
I would like to do DE analysis of RNAseq data.

I have two set of experiments done in two different time points, so there
is probably batch effect: let's say batch A and B.

For A, I have 7 controls and 7 cases (clinical identified)
For B, I have the same 7 controls and other 7 pre-cases (preclinical
identified)

I wanted to know if I can analyze all together, but I have questions like:


1-7 cases from A are only in batch A, and the others 7 are only in batch B,
is it correct to setup a blocked variable indicating the batch effect
although I only have one entire group for one batch, and another entire
group for another batch?
2-and 7 control for A and B are same people, so it is not quite right to
merge all together because it would be more like technical replicates.

My goal is:

1-get DE genes that follow additive effect. Something like increase a
little in pre-cases, and increase more in cases.

Thanks to all!

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