different number of samples from each individual

Question

[leranwangcs]

Hi,

In my dataset, the number of samples from each individual are different, something like this:

I want to compare active and inactive status, but as you can see, patient 1,2,3 has 1 samples in each status, whereas patient 4,5,6,7,8 contribute multiple samples in each status.

I wondered if I can just go ahead and do the comparison between active and inactive, without considering the different sample sizes from each individual? Or if this would be a problem and mess up my comparison result?

Thanks! Leran

[ATpoint]

What kind of assay is this? RNA-seq?

[leranwangcs]

Hi, this for microbiome data.

[Kevin Blighe]

Cross-posted: https://support.bioconductor.org/p/9144225/

[leranwangcs]

They are actually different, that one is a specific question for DESeq.

[Kevin Blighe]

Thank you.