Bioconductor Forum

dominance` function, > `x`: A species abundance vector, or matrix with the absolute count data (**no relative abundances**). This seems intended for 16S data analysis. How can a user calculate Simpson index for MetaPhlAn proportions

microbiome

updated 1 day ago • Dario Strbenac

Hi all. I am trying to run a pseudobulk analysis assessing differential gene expression between control and mutant cells of different cell types. When we previously assigned our cell types, our...Hi all. I am trying to run a pseudobulk analysis assessing differential gene expression between control and mutant cells of different cell types. When we previously assigned our cell types, our preproces…

DESeq2 celda

updated 2 days ago • JalapenoCornbread

effect in a cohort of bulk RNAseq from patients. As you can see below on my PCA (generated using all genes), I have three groups of samples : green and blue for patient samples done at the same place with one technology, purple...not_sig_Novogene_blueprint = not_sig_Novogene_blueprint)) # 2653 genes ## Run RUVg sequencing table_to_see = as.data.frame(counts(dds)) RUVg_test <- newSeqExpr…

DESeq2 RUVSeq RUVseq BatchEffect DES

updated 2 days ago • Alexandre

lib function? When I use this function to handle the data from TCGA-BLCA and TCGA-SKCM, there is no problem. But I met this problem when I handle the data from TCGA-BRCA. Could you please provide any suggestion and solution...n_alt_count = col_logical(), all_effects = col_character(), Allele = col_character(), Gene = col_character(), Feature = col_character(), Feature_type …

GDCRNATools TCGA

updated 3 days ago • glaciya2018

Hello, I am having a hard time interpreting the IHW and Shrinkage method results. I have read the paper, and also vignette and other various other question threads. I understand the purpose of the methods, however, not sure how to interpret their results. I have currently run a code: dds<- DESeqDataSetFromMatrix(countData = counts_DE_subset, …

DESeq2 RNAseq

updated 3 days ago • kcarey

and this is my output. There is not much variance; what can I conclude from this? I can see the WT clustering together but the mutant samples are not far apart from each other. I expected the WT samples to cluster together...TRUE), ncol = 4, nrow = 100) mutant_counts <- pmax(base_counts - mutant_modifiers, 1) # Ensure no zero counts # Combine wild type and mutant counts countData &…

DESeq2 RSTUDIO PCAtools

updated 3 days ago • Aaliya

Will Rsubread's Subjunc perform correctly on genes, such as KIT, which have variable-length exons? ![KIT Isoform Structure][1] I would like to count the reads supporting the...Will Rsubread's Subjunc perform correctly on genes, such as KIT, which have variable-length exons? ![KIT Isoform Structure][1] I would like to count the reads supporting the Q...KIT Isoform Structure][2] Simi…

Rsubread

updated 3 days ago • Dario Strbenac

Hi, I am running (to me) identical code for some clustering but despite fixed seeds it is inconsistent when using either lapply or bplapply: Any idea what is happening? ``` suppressMessages...Hi, I am running (to me) identical code for some clustering but despite fixed seeds it is inconsistent when using either lapply or bplapply: Any idea what is happening? ``` suppressMessages({ li…

scran BiocParallel bluster

updated 3 days ago • ATpoint

lt;- res_h_d_ver2_noShrink %>% data.frame() %>% rownames_to_column(var='gene') %>% as_tibble() res_h_d_ver2_noShrink_tb <- merge(res_h_d_ver2_noShrink_tb, vM34annot, by.x='gene', by.y='ensgene') sig_h_d_up_ver2...lt;- ordered_sig_h_d_ver2$symbol sig_h_d_ver2_ensname <- ordered_sig_h_d_ver2$gene for (i in 1:29){ DEG_h_d_ver2[[i]] <- plotCounts(dds_h…

DESeq2

updated 4 days ago • winwater0928

I'd appreciate it if you could answer politely. I have a problem translating Ensembl ID to Entrez Gene ID. I've tried the script provided below, but although it runs without errors, it only returns "NA" in the entrezgene_id column...filters = "ensembl_gene_id", values = gene, mart = ensembl, useCache = FALSE

ensembldb

updated 4 days ago • Fara

Hi all, Does any one know how to obtain the information under GO class (direct) given a gene list? Ideally I would like to be able to retrieve it with R / API. I have tested several packages but none are able to retrieve

GO.db goTools

updated 4 days ago • bandconductor

that we are not trying to find the difference in decay rate between two conditions, but rather rank genes by their decay rate in a single condition. That is, in the above model, we are interested in ranking genes by the `b` coefficient...have sequenced every molecule present in our cDNA tube) we don't expect counts from highly expressed genes to crowd out counts from lowly expressed genes. This i…

DESeq2

updated 4 days ago • i.sudbery

Hello guys. I want to download cannabis orgdb using AnnotationHub, but when I try to use at enrichGO and others packages it doesn't work. What I can do? ``` > library(AnnotationHub) > hub <- AnnotationHub() snapshotDate(): 2023-10-23 > query(hub, c("cannabis","orgdb")) AnnotationHub with 1 record # snapshotDate(): 2023-10-23 # names(): AH114845 # $dataprovider: ft…

KEGGgraph org.Cs.eg.db clusterProfiler KEGG AnnotationHubSoftware

updated 4 days ago • fernanda.backsouza

the last step of metagenomic data processing, featurecounts kept reporting errors, and there was no output result file. Error message displayed:"featureCounts: input-files.c:2890: SAM_pairer_get_next_read_BIN: Assertion...t exon -g gene_id bwa/*.bam" I have checked line 2890 of the bam file and I think there should be no problem with it, I don't know the cause of this error, I would appreciate…

metaMSdata

updated 5 days ago • shuwangxinze1996

Hello, I have a dataset of *n* individuals which have been profiled using RNAseq in two conditions, *c1* and *c2*. For each individual, I want to get the logFC between these conditions, after

limma RNASeq voom

updated 5 days ago • taur.vil

dispersion: ```r dds_pois <- DESeq(dds_pois) estimating size factors estimating dispersions gene-wise dispersion estimates mean-dispersion relationship -- note: fitType='parametric', but the dispersion trend was not

DESeq2

updated 5 days ago • WardDeb

The "guide to creating design matrices for gene expression experiments" of the [RNAseq123 workflow][1] doesn't show some figures. Figure 3 and figure 13 show the html code

RNAseq123

updated 6 days ago • Lluís Revilla Sancho

the following errors. I have tried downloading the files directly from https://ftp.ncbi.nlm.nih.gov/gene/DATA/ after deleting the NCBI.sqlite file, but to no avail. I even tried changing the timeout settings to 10000. Any help...3] gene2refseq.gz [4] gene_info.gz [5] gene2go.gz getting data for gene2pubmed.gz Error: no such table: main.gene2pubmed > list.files() [1] "gene_info.gz" …

OrgDb AnnotationForge

updated 6 days ago • Gayatri

enrichGO from clusterProfiler, but I don't know what I doing wrong. Here my script: enrichGO( gene = ortologos_filtrados$Name, OrgDb = org.Cs.eg.db, keyType = "ENTREZID", ont = "MF", pvalueCutoff = 0.05, pAdjustMethod = "BH", universe...10, maxGSSize = 500, readable = FALSE, pool = FALSE ) ``` I'm using a vector in "gene" and "universe". …

clusterProfiler GenomicDistributionsData KEGG

updated 6 days ago • fernanda.backsouza

Hi all, I have a question that don't know why, hope you can help. I use GSVA (Gene Set Variation Analysis) package to calculate pathway scores. Then I compare pathway scores between 3 groups using limma

limma

updated 7 days ago • Chris

Enter the body of text here Code should be placed in three backticks as shown below ```r features <- binGenome( genomeTxDb ) # include your problematic code here with any corresponding output features <- binGenome( genomeTxDb ) 64 genes were dropped because they have exons located on both strands of the same reference sequence or on more than one reference se…

ASpli

updated 7 days ago • Sebashish

Enter the body of text here Code should be placed in three backticks as shown below ```r features <- binGenome( genomeTxDb ) 64 genes were dropped because they have exons located on both strands of the same reference sequence or on more than one reference sequence, so cannot be represented by a single genomic range. Use 'single.strand.genes.only=FALSE' to get all the g…

ASpli

updated 7 days ago • Sebashish

Hi all, I noticed there are many questions and no dedicated tutorials here for installing multiple versions of R and bioconductor so I thought I''d share how I install and...Hi all, I noticed there are many questions and no dedicated tutorials here for installing multiple versions of R and bioconductor so I thought I''d share how I install and switch between versions of R and bioconductor on …

bioconductor Install

updated 8 days ago • BioinfGuru

to be overly conservative but I also want to adequately control for type-1 errors. Note, there is no problem with my r code, I understand how to apply each FDR procedure, I'm just finding it difficult to find oncrete infromation

qvalue

updated 8 days ago • John

I have a list of gene symbols for which I want to retrieve the Ensembl Gene ID. I have a dataframe (df_biomrt_tmp) containing a column with the...I have a list of gene symbols for which I want to retrieve the Ensembl Gene ID. I have a dataframe (df_biomrt_tmp) containing a column with the symbols and after running ```r df_biomrt_tmp-> getBM(attributes = c("hgnc_symbol", "ensembl_gene_i…

biomaRt

updated 8 days ago • bas_work

How to make DGEList and design matrix for that. I want to get DEGs (differentially expressed genes) between Mr-Mf, Br-Bf, Er-Ef. Thank you in advance for your input

DGEList edgeR

updated 9 days ago • prity6459

not supported, could anyone suggest something to resolve this? ``` ora_analysis_BP <- enrichGO( gene = annot_diff$entrezgene_id, universe = annot_universe$entrezgene_id, OrgDb=maize , keyType = "ENTREZID", ont = "CC", pAdjustMethod

clusterProfiler OrgDb biomaRt Zea_mays

updated 9 days ago • sansan

log fold change. Then I order the vector from decreasing to increasing values so the downregulated genes are at the top while the upregulated genes are at the bottom. This is shown in the code below: ```r newRank_pvalueAndFC = -log10...newRank_pvalueAndFC[order(newRank_pvalueAndFC)] ``` In other words, the downregulated genes with a really small fdr value are at the top and the upre…

fgsea

updated 9 days ago • sropri

the sample names are Mf, Bf, Ef, Mr, Br, and Er. I want to get DEGs (differentially expressed genes) between Mr-Mf, Br-Bf, Er-Ef. For doing that, I subsetted my data keeping either Mr-Mf, Br-Bf, or Er-Ef. And then I got DEGs for three..._epidermis.csv", header = TRUE, row.names = 1) # Since the data is already normalized, there is no specific step for normalization # Extract Mf and Mr s…

subsettingdata edgeR designmatrix

updated 9 days ago • prity6459

to the one I am using now (ensembl release 111). The previous version reports 36 exons for my gene of interest (myo6), while the one I am using reports 73 exons. The exons I am looking for in silico were previously validated...2. treatment 2 vs control And the output is then composed by two tables. However, the results are no longer significant for the exons of interest, while they were in …

DEXSeq

updated 9 days ago • Alessia

analysis, linux, R script and don't exactly trust myself when doing analysis of RNAseq data but no one else in my lab has experience either! I am doing my PhD and now find myself with 3 datasets to analyse and I would like to...lung(model1), lung(model2-reflects different phenotype of disease). I have removed adapters, then mapped reads to genome and transcriptome respectively using Minimap2, thi…

DESeq2 LongRead DEXSeq IsoformSwitchAnalyzeR RNASeq

updated 9 days ago • 09191919

filter differently, e.g., by taking some minimal `AveLogCPM` from the entire cohort? * Or only genes that pass a certain `AveLogCPM` from **BOTH** *X* and from *Y*? * Or perhaps genes that `AveLogCPM` pass each of the 7 subgroups independently

edgeR

updated 10 days ago • Jonathan

Hello, I am using DEseq2 to analyze the relationship between gene expression and two continuous phenotypic predictor variables, one of which has both positive and negative values...Hello, I am using DEseq2 to analyze the relationship between gene expression and two continuous phenotypic predictor variables, one of which has both positive and negative values. Is

DESeq2

updated 11 days ago • Brynn

object? I ran DEXSeq on a transcriptome assembled with [Trinity][1], so it has trinity_ids as gene symbols. However, these are not ideal to show on plots, so I ran blast and got some gene symbols. Now I want to add the column...of gene symbols to the DEXSeqResults object before running plotDEXSeq but I am not sure how best to do so. I have tried converting...object ``` # Load RData file load("…

DEXSeq

updated 11 days ago • Clyde

to run the gseGO function in clusterpofiler to look at GSEA of my list of differentially expressed genes. The structure of the data is the following: ``` X baseMean log2FoldChange lfcSE stat pvalue padj 1 MAGEA4 85.001287 10.406827...4.816262 1.46000e-06 0.005414319 ``` I perform the following transformations to extract the gene list (I have trie…

clusterProfiler GeneSetEnrichment

updated 11 days ago • Ana

are `0 enriched terms found` when I performed the `enrichGO()` function on the tumor and normal gene lists containing the respective entrez ID of the differentially enriched genes. May I ask if anyone encountered a similar...Over-representation analysis ego_normal <- enrichGO(gene = entrez_normal, keyType = "ENTREZID", OrgDb = org.Hs.eg.db, …

ChIPseeker

updated 12 days ago • Henry

function), where I do not know the names (or the number!) of the extra columns to add, I again have no clue. I was hoping the answer to the previous question would apply to this too, and I almost got it, but still not quite there

ComplexHeatmap

updated 13 days ago • daniel.carbajo

Hi I am currently analyzing RNASeq data, having used HISAT2 for mapping and StringTie for quantification. I've proceeded to use DESeq2 for differential expression analysis, but I've encountered...an issue where many of the differentially expressed genes (DEGs) identified are lowly expressed according to the count matrix. Could this suggest a potential error in my analysis

DESeq2

updated 13 days ago • Rajat

Hi I was wondering if there is any way to extract DEGs from monocle pseudotime trajectory. I want to extract DEGs for a particular pseudotime state vs all others. Is there any way to do so? Thanks!

monocle

updated 14 days ago • kthapa

3 different tissue and sequenced same time each individual has WT and KO data wanted differential gene expression tried read all question regarding design matrix still I am unable create design matrix any one please help

DESeq2

updated 15 days ago • hemantcnaik

Hi, From a Deseq2 analysis, I have just the final table of results (I guess res(dds)). My first question is if the counts there are normalized counts or just the counts for each gene from the initial data without any transformation? My second question is if I can do with just with these data outlier analysis...dds)). My first question is if the counts there are normalized counts or just t…

Des DESeq2

updated 15 days ago • Sahar

Hi! I have a gene list, ranked by log2FoldChange for the input of gseKEGG to return a kegg object or data frame that has info on enriched...pathways. However, I would like to know how many of my genes from my gene list are in each enriched pathway. How can I do this? Thank you

Pathways clusterProfiler gseKEGG KEGG

updated 15 days ago • julia_mcdonough

The Code Freeze for the current Bioconductor 3.18 Release is scheduled for next Monday April 15, 2024. After this date there will be no changes to the code on this branch; this includes bug fixes or hot fixes. If your package is failing on the release build report, this weekend will be your last chance ever to update the code on RELEASE_3_18 branch of Bioconductor. Software Report: https…

Release release Bioconductor Bioconducto

updated 15 days ago • shepherl

msg, call)) : error in evaluating the argument 'x' in selecting a method for function 'seqinfo': no 'header' line "#CHROM POS ID..."? ``` Checking the file on disk I can see the apparently missing header line ``` bash zcat new.vcf.bgz | head

VariantAnnotation

updated 16 days ago • Stevie Pederson

design = ~ cell + dex) dds <- DESeq(dds) ``` ``` estimating size factors estimating dispersions gene-wise dispersion estimates *** caught bus error *** address 0x100000cfeedfacf, cause 'invalid alignment' Traceback: 1: fitBeta

DESeq2

updated 17 days ago • Shefali

Hi there, I understand that DESeq2 uses GLM to regress over the raw gene count matrix. And I just wonder for the inner part of the linear regression, is it possible to retrieve some more detailed...calling this information out? b. Is there any function to retrieve the 'y' value matrix for each gene * each sample? I know vsd or log2(normalized counts) is quite similar to what I want, but I gue…

DESeq2

updated 17 days ago • Weiqian

in json text <html> <head><title>504 Gatewa" This happens only for a very small proportion of genes. It happens both when I either feed it a vector of gene symbols or when I manually write out the individual problematic...genes, as done below for "NFE2L2". When I fill in this gene in the online DGIdb, the gene exists and produces output. Any idea what...s happening here and …

lexicalerror rDGIdb DGIdb json

updated 17 days ago • Dennis

r dotplot( result_gsea_mitocarta, x = "NES", color = "p.adjust", showCategory = 8, split = "Cluster", font.size = 12, title = "", by = "NES", size = "Count", includeAll = TRUE, label_format = 30 ) + facet_grid(. ~ Cluster) + geom_vline(xintercept

DOSE enrichplot clusterProfiler

updated 17 days ago • Lucie

vs MYCN non amplified. Cell lines in the MYCN non amplified group had these FPKM values for MYCN gene: 5.182582, 3.104376, 4.962478 Cell lines in the MYCN amplified group had these FPKM values for the MYCN gene: 101.2204, 301.8182

limmaGUI edgeR limma

updated 18 days ago • Simran

I am currently performing a differential gene expression analysis containing 1000s of samples. The samples have 3 different genotypes and were treated either with

DESeq2 DifferentialExpression

updated 18 days ago • nhaus

Hi all, I have ~1000 RNAseq samples that come from 100 donors and am using edgeR to analyse it. The tissue from the 100 donors was treated with either 9 different chemicals (A, B, C, ...) or not treated at all (control). Unfortunatly, due to technical reasons, I had to remove some of the control condition (only 3) due to a low number of reads (<5e6). This means that I have some "un…

edgeR DifferentialExpression

updated 18 days ago • nhaus

I have some scRNA seq data, and I want to check and see which transcripts for a specific gene (it has about 5 alternative transcripts) are expressed in a specific cell type. Is that possible

scRNAseq RNAseq

updated 19 days ago • Merav

of new bioinformatics methods - Interpretation and publication of bioinformatic analyses **Your profile:** - Master degree in bioinformatics / computational biology or a related field, e.g., life sciences, informatics or mathematics...https://www.wpr.ruhr-uni-bochum.de/ If the position is funded by third-party funds the employee has no teaching obligation. German language courses are offere…

Mergeomics Epigenome Evolution NGS Aging

updated 19 days ago • arne.sahm

each with 3 biological repeats. I run my data through edgeR and obtained differentially expressed genes (DEGs). Due to the low sample number and small effect size, there are likely more genes affected by the treatment that didn...logFC or PValue) do I take from each permuted dataframe to generate the distribution for each gene and calculate the p-value? Also, what is the p-value calculation? T…

rna-seq edgeR

updated 20 days ago • Netanel

Our experts can continuously improve your development programs by building a series of advanced platforms. We are committed to being a trusted brand that delivers on our vision and continually reinforces our values and beliefs throughout the pharmaceutical industry. Details about [impurity identification][1] [1]: https://www.solutions.bocsci.com/impurity-isolation-and-identification.htm

metaMSdata

updated 21 days ago • 1768982493

the absolute value of the log2FC is the same --> so, genes that are in "control vs mutant" on top of the ranked list are in "mutant vs control" at the bottom of the list --> ranking exactly...in the inverse order. E.g. "control vs mutant": 1. Gene A log2FC 3 2. Gene B log2FC 0.5 3. Gene C log2FC -4 E.g. "mutant vs control": 1. Gene C log2FC 4 2. Gene B log2FC 0.5 3. Gene A lo…

clusterProfiler gseKEGG

updated 22 days ago • andromeda

DGE object][2] ``` dge <- DGEList(counts = Counts, group = sampleInfo$Group, genes = genes[which(rownames(genes) %in% rownames(Counts)),] ) ``` [1]: /media/images/e7926879-6b23-4f59-b89f-292c11b6 [2]: /media/images/8cb50a22

edgeR DifferentialExpression

updated 22 days ago • Shaimaa Gamal

2-10 + | 0 0 ------- seqinfo: 22 sequences from an unspecified genome; no seqlengths > ``` ``` R version 4.3.3 (2024-02-29) Platform: aarch64-apple-darwin20 (64-bit) Running under: macOS Sonoma 14.4.1 Matrix

methylKit

updated 22 days ago • Modoc Kesner

Hi as I understand it, in DESeq2 one of the ways to run a DEG analysis on time course data is using a likelihood ration test on two different models. For example, I can test for genes that show significant differences in time trajectories for two different treatments can be done as follows ``` ddsMat<-DESeqDataSetFromMatrix(countData=Xdata, coldata=DMAT, design= treatment+time+tr…

DESeq2 timecourse DifferentialExpression

updated 22 days ago • joshua.mannheimer

I know that Bluster leverages [igraph][1] to do clustering. Seurat has ordinary Louvain and "Louvain with multilevel refinement" (but no reference). Is there any way to get the

bluster

updated 23 days ago • Dario Strbenac