Tag: ANCOM-BC

DESeq2 (zeros in the taxa table) – Other Bioinformatics Tools

komal (Komalk) January 19, 2024, 12:02pm 1 Hi this is regarding DESeq2. I first created a phyloseq object from qiime2 artifacts and then subjected it to Deseq2. At one step I got a errorError in estimateSizeFactorsForMatrix(counts(object), locfunc = locfunc, :every gene contains at least one zero, cannot compute log geometric…

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Metaproteogenomic analysis of saliva samples from Parkinson’s disease patients with cognitive impairment

Characteristics of participants and analyses A total of 115 individuals (43 PDD, 45 PD-MCI) and 27 HC were included in this study. Both 16 S rRNA gene amplicon sequencing based microbiome analysis and metaproteomics profiling were performed for all salivary samples collected from the participants (Fig. 1). Fig. 1: Experimental overview….

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Higher abundance of Campylobacter in the oral microbiome of Japanese patients with moyamoya disease

A flow diagram of the study is shown in Fig. 3. Figure 3 Flow diagram of the study. Ethical approval and consent to participant This study was approved by the Institutional Review Board of the Nagoya University Graduate School of Medicine (approval number 2022-0084; approval date, June 3, 2022). Written informed…

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ANCOM-BC log-fold change direction discordant to feature table – General Discussion

Hi,I tried ANCOM-BC to do some analysis at feature level. In some cases, I found the value of log-fold change was discordant to feature table. For example, I had a feature with the log-fold change value of -0.159 not favoring the experimental group. But when I inspected into the feature…

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Ancom vs AncomBC? – Other Bioinformatics Tools

kkl45 (Kevin Lee) October 3, 2023, 12:52pm 1 I have shallow shotgun data that I am running Ancom and Ancom BC on. With Ancom i get several differentially abundant species but when i run ANCOM-BC with FDR correction, i lose all of the significant taxa. Im wondering how to weigh…

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Phage-microbe dynamics after sterile faecal filtrate transplantation in individuals with metabolic syndrome: a double-blind, randomised, placebo-controlled clinical trial assessing efficacy and safety

Study design We set up a prospective, double-blinded, randomised, placebo-controlled intervention study that was performed in our academic hospital, the Amsterdam University Medical Centres location AMC in the Netherlands. After passing screening, 24 subjects with MetSyn were randomised to receive a sterile FFT from a lean healthy donor or a…

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q2-ancombc on qiime2-2021.11 – Technical Support

Hi I tried to install q2-ancombc as described here GitHub – mortonjt/q2-ancombc: qiime2 plugin for ANCOMBC.R version 4.0.5 (2021-03-31) if (!requireNamespace(“BiocManager”, quietly=TRUE))install.packages(“BiocManager”)BiocManager::install(“ANCOMBC”)install.packages(‘tidyverse’) I noticed following errors ERROR: dependency ‘nloptr’ is not available for package ‘ANCOMBC’ERROR: dependency ‘ragg’ is not available for package ‘tidyverse’ I would appreciate if you could help…

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Nitrate and a nitrate-reducing Rothia aeria strain as potential prebiotic or synbiotic treatments for periodontitis

Bacterial strains and growth conditions Rothia aeria CECT9999 (Ra9, isolate D1P7 described in24), was used as a nitrate-reducing probiotic candidate. Prior to the experiment, Brain Heart Infusion (BHI) (Biolife, Deerfield, Illinois, USA) agar plates were inoculated with the strain, incubated for 48 h at 37 °C, and stored at 4 °C for up…

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Plugin error from ancombc (composition): colSums not exported by DelayedArray – Technical Support

This is a similar issue to this and this, but I have not been able to solve my case with the available information there. I am running qiime2 version 2023.2 in a conda environment. The problem was detected when I tried to run an analysis, but I could replicate the…

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ANCOM-BC OF THE METABOLIC PATHWAYS DIFFERENTIALLY ABUNDANT BETWEEN TREATMENTS: SUPPLEMENTARY RESULTS TABLE 2.5.2

Table S2.5.2: ANCOM-BC analysis showing the differentially abundant predicted metabolic pathways (MetaCyc) in the subsoil layer (3-4 cm beside the amendment). S2.5.2A: Planted soils with deep-banded amendment (DBA) compared to unplanted soils with DBA. S2.5.2B: Planted soils with DBA compared to planted soils without DBA. School School of Agriculture, Biomedicine…

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Low W taxa identified as significant – troubles with workaround – User Support

Dear community. I started working with Qiime2 (2023.2) recently and i am facing some issues with ANCOM/ANCOM-BC. I have read multiple posts in the forum and done the tutorials, but still not sure how to proceed. Originally, i was just running Alpha Diversity, Adonis and PERMANOVA test to analyze my…

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Problems with ANCOMBC Composition Plugin in Qiime2: CLI partially fixed, but Python API still problematic – Technical Support

It seems like the modifacation of the miniconda3/envs/qiime2-2023.2/lib/python3.8/site-packages/q2_composition/_ancombc.py file indroduced some of the Problems. Without my changes the CLI works! Unfortunately, the Python API problem persists. When running the code snippet below, the error message is still present: import qiime2 from qiime2.plugins.composition.actions import ancombc example = qiime2.Artifact.import_data(‘FeatureTable[Frequency]’, ‘example_data/ancombc-single-formula/feature-table.biom’) example_meta =…

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ancombc documentation

excluded in the analysis. Solve optimization problems using an R interface to NLopt. The overall false discovery rate is controlled by the mdFDR methodology we In this formula, other covariates could potentially be included to adjust for confounding. depends on our research goals. W, a data.frame of test statistics. enter…

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export ANCOM-BC normalisation matrix

Hello! I have similar doubt. Did you solve it? I run ancombc with my Phyloseq opbject and extract the data, but we are not certain about the normalization: out = ancombc(phyloseq = phyloseq_obj, formula = “condition_1”, p_adj_method = “BH”, zero_cut = 0.90, lib_cut = 1000, group = NULL, struc_zero =…

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