Question: batch correction in DESeq2 > matrix not full rank > mitigate
gravatar for MT
28 days ago by
MT0 wrote:

Hello, I am a novice and I am interested in comparing two kind of cells coming from different RNA sequencing experiments published. The design would be something like the following:

sample    cell    batch
1    type1    1
2    type1    1
3    type1    1
4    type1    2
5    type1    2
6    type2    3
7    type2    3
8    type2    3
9    type2    4
10   type2    4

Now, naturally I cannot model del batch effect with ~ batch + cell because the batch is nested in the condition "cell". But the question remains, what is the best way to compare type 1 and type 2 taking into consideration and mitigating possibile batch effects?

Thanks for your help. Best, Marco

deseq2 batch correction • 108 views
ADD COMMENTlink modified 28 days ago by James W. MacDonald52k • written 28 days ago by MT0
Answer: batch correction in DESeq2 > matrix not full rank > mitigate
gravatar for James W. MacDonald
28 days ago by
United States
James W. MacDonald52k wrote:

The short answer is that you can't do that. There's no way to resolve the confounding.

ADD COMMENTlink written 28 days ago by James W. MacDonald52k

Perhaps you can try surrogate variable analysis?

ADD REPLYlink written 26 days ago by cihan.erkut10

Surrogate variable analysis isn't magic, and won't fix confounding.

Think of it this way. If you had a study where you treated a group of patients with a drug and had a group of patients who were controls, but at the same time all of the treated patients were smokers and the controls were not, how would you ever know if any differences were due to the treatment or the smoking?

SVA is just a way to adjust out unobserved factors, but it won't help with completely confounded variables. There is no magic way to fix that.

ADD REPLYlink written 24 days ago by James W. MacDonald52k
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