Hi
I am very new to this microbiome analysis so this might be a very simple question... I have a question related to the microbiome analysis I'm doing. I have microbiome data from 3 different timepoints (T1, T7, and T13), for I made each time a phyloseq object. For each of the timepoints there are the same number of samples (IAM01-IAM30) for which I have (for now) available: gender, age.
I now want to plot a t-SNE plot where I have colors per gender, age-group and timepoint but I don't know how to merge the phyloseq objects?
I made first a dataframe with the ASV in the columns and the samples in the rows, and then the metadata next to it, for each timepoint. This I would then merge, but the ASVs ofcourse vary (ASV1 for timepoint 1 phyloseq object is different from ASV1 in timepoint 7).
Can someone help me out? Ideally I would need to have this kind of dataframe (cell = relative abundances/counts)
Thank you very much in advance!
Then, why did you analyzed each timepoint independently?
Hmm. I have a phyloseq object per time point seperately. I followed the DADA2 tutorial (starting from fastq files per sample, per time point) and ended up in this way in 3 different phyloseq objects. I still want to consider samples from different timepoints as being independent samples.
this DADA2 tutorial?
Yes, in which I analyzed the timepoints seperately. So I'm thinking to do this DADA2 tutorial maybe again, on all fastq samples and then afterwards extract the timepoint?
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