# \#normalization **URL:** https://forum.qiime2.org/tag/normalization/122.md [Latest](https://forum.qiime2.org/latest.md) · [Categories](https://forum.qiime2.org/categories.md) · [Tags](https://forum.qiime2.org/tags.md) --- ## [SRS as a normalisation method.](https://forum.qiime2.org/t/srs-as-a-normalisation-method/30531)
**Author:** [@MarwaTawfik](https://forum.qiime2.org/u/MarwaTawfik)\ **Replies:** 5\ **Last updated:** [July 1, 2024, 10:38pm UTC](https://forum.qiime2.org/t/srs-as-a-normalisation-method/30531 "2024-07-01T22:38:21Z")
Hi team I am interested to add SRS as a plug-in in qiime2 and would be appreciated if you could give me some guidance of how I can implement this as a plug-in in qiime2? Thanks in advance Marwa --- ## [Before I get into CLR transformation, is there any step to change my OTU table ?](https://forum.qiime2.org/t/before-i-get-into-clr-transformation-is-there-any-step-to-change-my-otu-table/25777)
**Author:** [@SingeunOh](https://forum.qiime2.org/u/SingeunOh)\ **Replies:** 8\ **Last updated:** [May 18, 2023, 4:21pm UTC](https://forum.qiime2.org/t/before-i-get-into-clr-transformation-is-there-any-step-to-change-my-otu-table/25777 "2023-05-18T16:21:31Z")
Hello ! Folks. I'm trying integrate OTU table data from different batches. Hence, I'm considering to do normalization before any further analysis. I have looked through normalization methods and found that Centered Lo… --- ## [Is it necessary to transform the read count data into relative abundance form before normalization when analyzing using two different ecosystems (different batches)?](https://forum.qiime2.org/t/is-it-necessary-to-transform-the-read-count-data-into-relative-abundance-form-before-normalization-when-analyzing-using-two-different-ecosystems-different-batches/25979)
**Author:** [@SingeunOh](https://forum.qiime2.org/u/SingeunOh)\ **Replies:** 2\ **Last updated:** [April 9, 2023, 11:51pm UTC](https://forum.qiime2.org/t/is-it-necessary-to-transform-the-read-count-data-into-relative-abundance-form-before-normalization-when-analyzing-using-two-different-ecosystems-different-batches/25979 "2023-04-09T23:51:56Z")
Hello! I am considering conducting a correlation analysis using a linear model and a heat map, as well as co-occurrence network analysis using samples from two different body sites in one host. The NGS run for each bod… --- ## [How can I change the Aldex .clr result in R to the table file which can be downloaded ?](https://forum.qiime2.org/t/how-can-i-change-the-aldex-clr-result-in-r-to-the-table-file-which-can-be-downloaded/25781)
**Author:** [@SingeunOh](https://forum.qiime2.org/u/SingeunOh)\ **Replies:** 2\ **Last updated:** [April 5, 2023, 12:11am UTC](https://forum.qiime2.org/t/how-can-i-change-the-aldex-clr-result-in-r-to-the-table-file-which-can-be-downloaded/25781 "2023-04-05T00:11:14Z")
Hello, I've tried to transform my ASV read count files to the CLR form by using R Aldex2 packages. I've got some results from it, but there is a problem. As below, the results are just shown line by line and there is n… --- ## [q2-repeat-rarefy: QIIME2 plugin for generating the average rarefied table for library size normalization using repeated rarefaction](https://forum.qiime2.org/t/q2-repeat-rarefy-qiime2-plugin-for-generating-the-average-rarefied-table-for-library-size-normalization-using-repeated-rarefaction/18032)
**Author:** [@yxia](https://forum.qiime2.org/u/yxia)\ **Replies:** 1\ **Last updated:** [March 22, 2023, 11:50am UTC](https://forum.qiime2.org/t/q2-repeat-rarefy-qiime2-plugin-for-generating-the-average-rarefied-table-for-library-size-normalization-using-repeated-rarefaction/18032 "2023-03-22T11:50:16Z")
q2-repeat-rarefy: QIIME2 plugin for generating the average rarefied table for library size normalization using repeated rarefaction When handling a sparse dataset, I noticed that the rare taxa were easily ignored by the… --- ## [Obtain normalized data - ANCOM](https://forum.qiime2.org/t/obtain-normalized-data-ancom/22021)
**Author:** [@JeremyTournayre](https://forum.qiime2.org/u/JeremyTournayre)\ **Replies:** 5\ **Last updated:** [February 4, 2022, 2:58pm UTC](https://forum.qiime2.org/t/obtain-normalized-data-ancom/22021 "2022-02-04T14:58:35Z")
Hello, Is it possible to get the normalized data after the normalization by ANCOM please? Thanks in advance, Jérémy Tournayre --- ## [q2-srs: QIIME2 plugin for library size normalization by scaling with ranked subsampling (SRS)](https://forum.qiime2.org/t/q2-srs-qiime2-plugin-for-library-size-normalization-by-scaling-with-ranked-subsampling-srs/17661)
**Author:** [@vheidrich](https://forum.qiime2.org/u/vheidrich)\ **Replies:** 3\ **Last updated:** [December 6, 2021, 8:14pm UTC](https://forum.qiime2.org/t/q2-srs-qiime2-plugin-for-library-size-normalization-by-scaling-with-ranked-subsampling-srs/17661 "2021-12-06T20:14:11Z")
Hi everyone, I am happy to announce that the SRS QIIME 2 plugin is out! SRS is an alternative library size normalization tool. For details, take a look at the SRS paper or go to the @lukasbeule's topic on how SRS works… --- ## ["z-score" for sparse data (taxon distribution)](https://forum.qiime2.org/t/z-score-for-sparse-data-taxon-distribution/20612)
**Author:** [@thedam](https://forum.qiime2.org/u/thedam)\ **Replies:** 1\ **Last updated:** [September 1, 2021, 2:45pm UTC](https://forum.qiime2.org/t/z-score-for-sparse-data-taxon-distribution/20612 "2021-09-01T14:45:03Z")
Hey, is there any "z-score" for sparse data like our count tables? I'd like somehow to compare how far a sample is from a group of samples; For example: I have my ASV table, and let's say I take a taxon on genus level: … --- ## [SRS: Alternative tool for library size normalisation](https://forum.qiime2.org/t/srs-alternative-tool-for-library-size-normalisation/16017)
**Author:** [@lukasbeule](https://forum.qiime2.org/u/lukasbeule)\ **Replies:** 16\ **Last updated:** [December 1, 2020, 8:33pm UTC](https://forum.qiime2.org/t/srs-alternative-tool-for-library-size-normalisation/16017 "2020-12-01T20:33:53Z")
Hi everyone, I am using QIIME 2 since 2017, spend countless days with reading in the QIIME 2 forum, and highly appreciate the community support! Moreover, I am an advocate of Open Science and, thus, feel at home in the … --- ## [Quantification and raw OTU abundance comparison](https://forum.qiime2.org/t/quantification-and-raw-otu-abundance-comparison/16927)
**Author:** [@Natalia\_Bednarska](https://forum.qiime2.org/u/Natalia_Bednarska)\ **Replies:** 2\ **Last updated:** [October 7, 2020, 9:28pm UTC](https://forum.qiime2.org/t/quantification-and-raw-otu-abundance-comparison/16927 "2020-10-07T21:28:20Z")
We’ve currently evaluated different microbial analysis software and wanted to get into quantification rather then qualitive measures of microbial diversity. I wanted to ask you, what is the best method to assess/express… --- ## [CSS normalization of sequence counts with metagenomeSeq in R](https://forum.qiime2.org/t/css-normalization-of-sequence-counts-with-metagenomeseq-in-r/4288)
**Author:** [@CarlyRae](https://forum.qiime2.org/u/CarlyRae)\ **Replies:** 3\ **Last updated:** [December 12, 2019, 9:35pm UTC](https://forum.qiime2.org/t/css-normalization-of-sequence-counts-with-metagenomeseq-in-r/4288 "2019-12-12T21:35:26Z")
All R code: TUTORIAL ON CSS normalization with metagenomeSeq BY: Carly Muletz Wolz Date: May 24, 2018 install metagenomeSeq, had some issues here, finally worked make sure all packages are up to date source("https://bio… --- ## [Normalization for microbiome 16s sequence analysis](https://forum.qiime2.org/t/normalization-for-microbiome-16s-sequence-analysis/10398)
**Author:** [@abalter](https://forum.qiime2.org/u/abalter)\ **Replies:** 7\ **Last updated:** [June 27, 2019, 6:55pm UTC](https://forum.qiime2.org/t/normalization-for-microbiome-16s-sequence-analysis/10398 "2019-06-27T18:55:42Z")
The way I understand things, normalization (such as in DeSeq2, EdgeR, etc.) serves two purposes: 1) Model the "real" abundance in the original samples from the read counts, 2) Make the abundance distributions conform to … --- ## [Use of rarefacted Table](https://forum.qiime2.org/t/use-of-rarefacted-table/9708)
**Author:** [@m\_max](https://forum.qiime2.org/u/m_max)\ **Replies:** 3\ **Last updated:** [May 15, 2019, 10:17am UTC](https://forum.qiime2.org/t/use-of-rarefacted-table/9708 "2019-05-15T10:17:52Z")
Hi, I have a question regarding the use of rarefacted tables. I know that such tables are commonly used only for diversity analysis while are not used as base for other analyzes like differential abundance or network con… --- ## [How to normalize bacterial abundance for unequal sample size?](https://forum.qiime2.org/t/how-to-normalize-bacterial-abundance-for-unequal-sample-size/7358)
**Author:** [@steffi](https://forum.qiime2.org/u/steffi)\ **Replies:** 8\ **Last updated:** [December 12, 2018, 10:01am UTC](https://forum.qiime2.org/t/how-to-normalize-bacterial-abundance-for-unequal-sample-size/7358 "2018-12-12T10:01:06Z")
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,… --- ## [Way to normalization OTU tables](https://forum.qiime2.org/t/way-to-normalization-otu-tables/6017)
**Author:** [@1115](https://forum.qiime2.org/u/1115)\ **Replies:** 2\ **Last updated:** [September 14, 2018, 12:22pm UTC](https://forum.qiime2.org/t/way-to-normalization-otu-tables/6017 "2018-09-14T12:22:23Z")
Hi to all! I have several OTU tables from each study raw data. What I want to do is to compare 2 different OTU tables so as to get some information whether there is a difference between studies under different situation… --- ## [Wisconsin standardization on rarefied data?](https://forum.qiime2.org/t/wisconsin-standardization-on-rarefied-data/5436)
**Author:** [@Fabs](https://forum.qiime2.org/u/Fabs)\ **Replies:** 1\ **Last updated:** [August 6, 2018, 11:21pm UTC](https://forum.qiime2.org/t/wisconsin-standardization-on-rarefied-data/5436 "2018-08-06T23:21:13Z")
Hi Mehrbod, I have a followup question. I was looking at some work I have done using NMDS for a statistics class, and we standardized the data using Wisconsin double standardization. So my question is, do you happen to … --- ## [Normalization use](https://forum.qiime2.org/t/normalization-use/4708)
**Author:** [@enricca](https://forum.qiime2.org/u/enricca)\ **Replies:** 5\ **Last updated:** [June 28, 2018, 7:13pm UTC](https://forum.qiime2.org/t/normalization-use/4708 "2018-06-28T19:13:03Z")
Why is it necessary to normalize by number of reads, if we use relative abundances? When we convert from absolute to relative abundances, aren't we performing some sort of normalization? (in fact, it is like performing M… --- ## [Batch Correction - Dealing With Negative Values for Diversity Analysis](https://forum.qiime2.org/t/batch-correction-dealing-with-negative-values-for-diversity-analysis/4262)
**Author:** [@Zachary\_Bendiks](https://forum.qiime2.org/u/Zachary_Bendiks)\ **Replies:** 9\ **Last updated:** [May 30, 2018, 12:52am UTC](https://forum.qiime2.org/t/batch-correction-dealing-with-negative-values-for-diversity-analysis/4262 "2018-05-30T00:52:03Z")
Hello, I am analyzing a dataset containing samples from two separate sequencing runs. I processed the reads identically, including trimming the same number of bases off the ends during the DADA2 step, before merging th… --- ## [Can we get the centered log ratio transformed feature table in qiime 2?](https://forum.qiime2.org/t/can-we-get-the-centered-log-ratio-transformed-feature-table-in-qiime-2/3505)
**Author:** [@junfei\_guo](https://forum.qiime2.org/u/junfei_guo)\ **Replies:** 2\ **Last updated:** [March 22, 2018, 7:45pm UTC](https://forum.qiime2.org/t/can-we-get-the-centered-log-ratio-transformed-feature-table-in-qiime-2/3505 "2018-03-22T19:45:20Z")
Hi, we are trying ancom step in Qiime 2 and found we can get the final volcano plot and statistical results. Is there any methods that we can get the centered log ratio transformed feature table? Thanks! Junfei --- ## [Is there a normalized\_table.py in QIIME2?](https://forum.qiime2.org/t/is-there-a-normalized-table-py-in-qiime2/475)
**Author:** [@Hanna](https://forum.qiime2.org/u/Hanna)\ **Replies:** 7\ **Last updated:** [March 9, 2018, 4:06pm UTC](https://forum.qiime2.org/t/is-there-a-normalized-table-py-in-qiime2/475 "2018-03-09T16:06:31Z")
Hi, I performed normalization of OTU table for downstream analysis using CSS or DESeq. I know QIIME2 work with sequence variants not OTUs using DADA2. I wonder if 100%OTUs of the sequence variants do not need the norm… --- ## [DESeq2/metagenomeSeq support for QIIME2](https://forum.qiime2.org/t/deseq2-metagenomeseq-support-for-qiime2/2121)
**Author:** [@jroth002](https://forum.qiime2.org/u/jroth002)\ **Replies:** 2\ **Last updated:** [December 22, 2017, 6:15pm UTC](https://forum.qiime2.org/t/deseq2-metagenomeseq-support-for-qiime2/2121 "2017-12-22T18:15:42Z")
Hi QIIME devs, Would it be possible to incorporate a plug-in in the future so that we can run DESeq2 or metagenomeSeq fitzig for differential abundance without having to export the feature table to QIIME1 or R? It woul… --- ## [Normalization necessary when converting to relative frequencies?](https://forum.qiime2.org/t/normalization-necessary-when-converting-to-relative-frequencies/1669)
**Author:** [@njnealon](https://forum.qiime2.org/u/njnealon)\ **Replies:** 1\ **Last updated:** [October 31, 2017, 12:17am UTC](https://forum.qiime2.org/t/normalization-necessary-when-converting-to-relative-frequencies/1669 "2017-10-31T00:17:44Z")
Hello! Just a follow-up to this... I downloaded the .csv files from my taxa barplots visualization (for each of the seven levels of taxonomies). I agree with hand-calculating relative frequencies. However, I just want to…