Hello everyone and thanks for having a look.
So I am currently writing my master thesis about the effects of 2 different radiations under differing oxygen levels on lung cancer cells.
I am only doing bioinformatics work the data already exists.
Now I have the following design we have 3 different oxygen treatments hypoxy(H), normoxy(N) and a group where the level was first low then normal (R).
And those are paired with 2 different radiation levels 0 or 8gy.
One run of it was made with xrays the other half a year later with ion radiation.
From the quality control I know that the gene expression in the control groups differs (0gyN vs 0gyH) since radiation is not a factor we would expect them to be similar but they are not between the two experiments. We also think we know why the oxygen sealing in the Carbon ion radiation experiments was different and apparently less good in keeping samples in hypoxy.
Now the question is can I still put both experiments in to DEseq as one matrix and just treat them as different batches to get direct comparisons, of course noting down that this is a problem with the data. So basically just treating the different seals and the resulting differences in hypoxy as part of the batch effect.
Or should I analyse the two experiments separately and only do a comparison of the results in more of a qualitative way?
Thanks a lot for your help I am happy to learn.
