# Use of rarefacted Table **URL:** https://forum.qiime2.org/t/use-of-rarefacted-table/9708 **Category:** General Discussion **Tags:** normalization, otus, rarefaction **Created:** [May 10, 2019, 9:32am UTC](https://forum.qiime2.org/t/use-of-rarefacted-table/9708 "2019-05-10T09:32:19Z") **Posts on this page:** 1 **Showing post:** 2
### Author: ![jwdebelius](https://forum.qiime2.org/user_avatar/forum.qiime2.org/jwdebelius/32/9655_2.png) [@jwdebelius](https://forum.qiime2.org/u/jwdebelius) #### Post date: [May 11, 2019, 9:32pm UTC](https://forum.qiime2.org/t/use-of-rarefacted-table/9708/2 "2019-05-11T21:32:48Z")
Hi @m_max, Welcome! There's been a fair bit of discussion around rarefaction here (or maybe Im just involved in a lot of them). It's maybe good to go look into those threads since they'll give you a wide variety of view points. Here are a few to start that I found pretty quickly. > [@How to normalize bacterial abundance for unequal sample size?](https://forum.qiime2.org/t/how-to-normalize-bacterial-abundance-for-unequal-sample-size/7358): > > Dear All, Ive executed QIIME2 analysis for my four different group. Each group consists of unequal sample size. Group A: 11 Group B: 9 Group C: 31 Group D: 12 and the sequence counts of each sample varies from 182,014 to 4,194. And I got more abundance in Group C for most of the taxa. In which way I can normalize the samples and get the abundance of taxa? Should I do any FPKM/RPKM or log2 normalization method ? Is there any R or some other tools to normalize OTU abundance. > [@Rarefraction not advantageous to detect differences in beta-diversity](https://forum.qiime2.org/t/rarefraction-not-advantageous-to-detect-differences-in-beta-diversity/1612/5): > > Hi @Alfred.Burian, Thanks for bringing this up! Without wading too far into this debate, I will point out that [rarefying is not always inadmissible](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5335496/), particularly for unweighted UniFrac and other beta diversity methods based on presence/absence of features. This is actually also shown in Fig 4 of the article that you posted, though for other distance methods other normalization strategies perform better. Second, what you describe is the qiime diversity core-metrics-phylogenetic method, which r… > [@Making sense of diversity estimates](https://forum.qiime2.org/t/making-sense-of-diversity-estimates/8916): > > What would you make of a dataset that, when you run said OTU table through Vegan to calculate distances using defaults (Method==Bray, Binary = FALSE) and depending on whether you filter based on per-sample ASV abundances, you get very different pictures? For example: Data is processed with Cutadapt and DADA2 defaults, then... Situation-1. incorporate all reads of any abundance \> 1 Situation-2. Require per-sample ASVs abundance \> 100 Now calculate distances, and run metaMDS... The distances… > [@Filter by group or entire dataset?](https://forum.qiime2.org/t/filter-by-group-or-entire-dataset/8783): > > In general, would it be advisable to filter by group if your dataset contains multiple sample types? For example, when working with data from one sample type, I typically filter features that are not found in \>95% of samples. I'd like to do this same type of filtering but the dataset I'm working with now is a composite from multiple body sites and environmental samples. All were run on the same lane, so I know that cross-talk might be a problem, and I can handle that by filtering features that … > [@Are there alternatives to rarefying for alpha diversity estimation?](https://forum.qiime2.org/t/are-there-alternatives-to-rarefying-for-alpha-diversity-estimation/7474): > > Hi Nick ! I disagree with the use of a rarefied table for alpha diversity estimation. Is there a better explanation why one should use a rarefied table for alpha-diversity estimates? > [@Alpha/beta diversity: filtering datasets, additional metadata post analysis and missing metadata values](https://forum.qiime2.org/t/alpha-beta-diversity-filtering-datasets-additional-metadata-post-analysis-and-missing-metadata-values/5832): > > Hi Qiime community, I am preparing to run the alpha and beta diversity metrics on my 16S V4 dataset but had a couple questions about the set up to answer the questions of my study. My study consists of sampling bacteria populations in lake water samples across 3 lakes and from 3 size fractions per lake ( whole water, \>20um and \<20um). Each lake was sampled once a week for several months. First I would like to look at how the diversity of the bacteria populations vary between lakes and between… Best, Justine --- _[View the full topic](https://forum.qiime2.org/t/use-of-rarefacted-table/9708)._