Hi
I have a question on the rarefaction curve that I have for my dataset. I have a dataset with microbiome samples for 3 timepoints. For timepoint 1 however, there is a median number of reads of 9265 (mean 9100), whereas for timepoint 2 and 3 I have respectively a median nr of reads of 76 049 (mean 77913) and 113 255 (mean 107898). I would like to make use of all timepoints, but I don't know how I should deal with that. In the rarefaction curve, with minimum sample size of 10 000 reads, not all curves reach a plateau. Also, when we would like to keep all samples from timepoint 1, then the diversity is quite low. I don't know what might be the best approach here? I read on this ComBat and removebatcheffects of Limma. I think this is an approach that might be helpful? Are there any (dis)advantages for these methods?
Thank you in advance!
It would be helpful to clarify additional information about your study design and what you think might be causing the observed source(s) of variation.
Hi there. I was wondering, how did you make it? Could you share your code, please?