Bioconductor Forum

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 24 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 24 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 24 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 25 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 25 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 25 days ago • Ana

Hi there! I'm trying to perform gene ontology analysis comparing tumor and normal samples. There are about 250 and 350 differentially enriched peaks in...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...anno) tumo…

ChIPseeker

updated 26 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 27 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 27 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 28 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 29 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 29 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 29 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 4 weeks 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 4 weeks 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 4 weeks 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 4 weeks 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 4 weeks 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 4 weeks 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 4 weeks 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 4 weeks 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 4 weeks 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 4 weeks 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 4 weeks 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 4 weeks 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 5 weeks 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 5 weeks 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 5 weeks 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 5 weeks 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 5 weeks 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 5 weeks ago • Dario Strbenac

Hi all, Im wondering if its possible to meaningfully combine data from EPIC and EPICV2 arrays. I have a MSet from each array, however, when I use combineArrays I end up with 0 probes. When I compared the two arrays for shared probes by removing the last part of the EPICV2 probe IDs ( ex. cg25324105_BC11 -> cg25324105), I figure that I should have about 726,890 shared probes. Is this …

EPICV1 Methylation combineArrays minifi EPICv2manifest

updated 5 weeks ago • Kim

With step-by-step, Log2FoldChanges seem to be the same, but padj and others are not, for each gene, exactly the same, and I have very slightly less DE genes. Is my **step-by-step not strictly equivalent to DESeq()** ? If so, do you see

DESeq2 Normalization

updated 5 weeks ago • RL

Hi, I'm investigating changes in gene expression after a body weight loss intervention. The data includes baseline measurements and two follow-up measurements

limma

updated 5 weeks ago • jari.karppinen

this beta coeficient and substracting it from the normalizes counts. I do get a very nice PCA clustering by Exposure condition. But I wonder if this preprocessing of the data is correct. A2) Regarding WGCNA, the free scale...for my conditions, but is this ok? B1) I also tried normalization with DEseq2 but the PCA clusters are by line and not by exposure. I wonder if I can correct for the li…

Voom Limma WGCNA

updated 5 weeks ago • Gimena

While doing the gene mapping from Affymatrix ids, I found out that there are multiple affymetrix IDs corresponding to a single gene name for...While doing the gene mapping from Affymatrix ids, I found out that there are multiple affymetrix IDs corresponding to a single gene name for a sample. My work revolves around gene names only. Please suggest the appropriate step to deal with this situation.…

biomaRt

updated 5 weeks ago • Reeya

I am seeing a very odd low dispersion group of genes. They seem to be distinct from the minimum dispersion genes that have come up in other questions (https://support.bioconductor.org...p/9149491/). Has anyone seen anything like this? I also tend to see a set of genes with inaccurately estimated log2FoldChange. It does not seem to be related to dispersion, however. For more information...u…

DESeq2

updated 5 weeks ago • Aidan

Hi, I generated some input data with Bismark, with the following code: ``` bismark_methylation_extractor -p --scaffolds --bedGraph --buffer_size 40G --genome_folder /home/juaguila/Bismark/ --cytosine_report --parallel 10 ${base}.deduplicated.bam ``` I want to identify differentially methylated region with dmrseq, and I tested a few files if they could be read by bsseq properly. ``` files &…

bsseq methylation

updated 5 weeks ago • ja569116

arabidopsisi is easier because there is the package for it how can I us a code like this if there is no package for Brachypodium. Can I create and object with a link to the enable plants brachy genome or which data I should download...model plant as brachypoidum dystachion? Thanks for your time and your help. ```r enrichGO(gene = de_genes, universe = all_genes, …

EnrichmentBrowser BrachypodiumDB RNASeqData

updated 5 weeks ago • Leyre

donors and for the library preparation batch effect. I am then looking for differentially expressed genes between post-prime and pre-prime, and post-boost and pre-boost, for each vaccine separately. I would like to plot boxplots...and a heatmap of the differentially expressed genes and for this I require corrected counts. I have currently used ComBat as follows. ``` group <- paste(donor,…

ComBat sva edgeR

updated 5 weeks ago • Lucy

Hello! I am new to Gene Ontology. I have a couple of lists of common DEG's from a couple of diseases. I want to shortlist the number of genes to get...candidate genes using gene ontology. I am looking for using David tool or shiny go tool for analysis. Can someone help me out in understanding...how to get enriched terms (how to interpret the charts and results obtained from gene ontology…

microbiomeExplorer

updated 5 weeks ago • Bhawna

with different feature assignments, namely assigning reads to genes, purely exonic regions, and purely exonic regions but assigning to the set of isoforms with which the read was consistent...examples, in all cases instances where the read completely and unambiguously overlaps an annotated gene that it should be assigned to: **Instances where read is assigned in all cases** ![Read assigned to g…

featureCounts Rsubread

updated 5 weeks ago • isaac.vock

Hello all! I have internet problem running the Bioconductor packages like GEOquery or getGEO command in Rstudio inside IRAN...(Iranian ip) There is no connection problem as other packages get installed flawlessly.. **If anyone has a solution or a working proxy it would be appreciated...packages like GEOquery or getGEO command in Rstudio inside IRAN...(Iranian ip) There is no connection proble…

No_internet_connection_Packages Proxy Bioconductor GEOquery Internet_connection_problem

updated 6 weeks ago • needNGS

obtained from aligning nanopore transcriptome sequencing data to the cdna sequence. To visualize gene models etc (in IGV) I need to convert it to genomic coordinates and I was wondering how can I be able to do it using ensembldb

ensembldb transcriptome genome coordinateconversion

updated 6 weeks ago • saadmurtazakhan

pathway score (from GSVA tool) between 3 conditions (normal control, early state, late state), I got no difference. Each condition have multiple samples. But when I remove early state observation from the data matrix, there

limma

updated 6 weeks ago • Chris

data. [estimateCellCounts] Processing user and reference data together. [preprocessQuantile] Mapping to genome. Error: useNames = NA is defunct. Instead, specify either useNames = TRUE or useNames = FALSE. In addition: Warning

min minfi

updated 6 weeks ago • clacarion

Hi, I am trying out some packages for PCA in combination with the reads-to-genes edgeR-workflow for my RNA-seq analysis. I used the directions given from this post: https://support.bioconductor.org...pch, col=colors, ncol=2) ``` I get this plot: ![plotMDS_Output][1] And although there is no clear clustering of the quartiles, it is pretty clear that there is some clustering going on. …

edgeR PCAtools

updated 6 weeks ago • Fabian

I have excel files contain gene count. Can i compare DEGs between two sets of group how can i perform analysis further ??? Can statistically it can be performed

metaMSdata edgeR

updated 6 weeks ago • Faisal

Hi, I used the following code to 1) get the significant genes that change based on time of day using LRT, 2) vst transform the data and find clusters based on their expression pattern...across the four timepoints (the ZTs). What I found confusing was that there were a few genes (not sure how many in total, but so far I noticed some) that did not exist in objects "dds_Time.lrt" or "cluster_rld", b…

DESeq2

updated 6 weeks ago • Mikushi

I am using WGCNA to analyse gene expression in airway biopsies from asthmatics and controls The standard WGCNA analysis gives clear correlations

Regression WGCNA

updated 6 weeks ago • w.cookson

Hi all, I'm new to **diffbind**. I've been given a set of **ATAC-seq** data computed with [nf-core/atacseq][1] and asked if there is any peak associated with the sex of the individuals. In my samplesheet i set the following columns: * **Tissue** tissue1 || tissue2 || tissue3 * **Condition** M || F # male of female * **Factor** NA my workflow , copied from a former co…

DiffBind ATACSeq

updated 6 weeks ago • Pierre Lindenbaum

Hi, Why I am not getting Up and Down regulated genes? My script is as below m I missed something or doing wrong ? ``` getGEOSuppFiles("GSE18090") ``` Untar and ReadAffy(rawdata). ``` gse...Hi, Why I am not getting Up and Down regulated genes? My script is as below m I missed something or doing wrong ? ``` getGEOSuppFiles("GSE18090") ``` Untar and ReadAffy(rawdata). ``` gse &lt

limma DGEanalysis

updated 6 weeks ago • Amit

has a different number of rows because the gtf files used to create them have a different number of gene annotations. Ideally, I would want my resulting merged file to have all of the columns from each of the 4 count files but

rnaseqGene

updated 6 weeks ago • Christian

the different species (including the 3 replicates) in the condition B set to see if certain species cluster together, i.e. they respond similar to the condition B. For that I have identified ~2500 single copy orthologues (orthologous...groups that have only one gene in all species), so there are ~2500 orthologous genes across species. I was planning to filter the table of raw counts (previously..…

DESeq2

updated 6 weeks ago • Laura

Max indel length : 5 || || Report multi-mapping reads : yes || || Max alignments per multi-mapping read : 1 || || Annotations : gencode.vM34.annotation.gtf (GTF) || || || \\===========…

Rsubjunc Rsubread

updated 6 weeks ago • thomas.heigl.ibk

objects. Here, I extract all the pairs which overlap either with the start or with the end of the gene. Then i extract the names of the overlapping range from their respective dataframe by merging the start and end positions...end")) ``` But this results in pairs that have overlap with either the start or end of the gene upto 10000 bps. However, I want them to have exact 10,000 bp distanc…

genomeIntervals GenomicRanges

updated 6 weeks ago • gshweta95

uses `SCTransform` followed by centring and scaling, each followed by their own conventional clustering variety. Is there any direct comparison of these two alternatives, perhaps on simulated data with a known truth

scran bluster scater scuttle

updated 6 weeks ago • Dario Strbenac

I was trying to run the function `runPCA()` but I got the error ```r function 'sexp_as_cholmod_sparse' doesn't exist in the package 'Matrix' ``` I looked online and found that installing `Matrix` and `irlba` from source is a solution. However, I wasn't able to do so due to this error ```r process_begin: CreateProcess(NULL, basename irlba.dll .dll, ...) failed. C:/PROGRA~1/R/R-43~1.2/share/make…

scater runPCA

updated 6 weeks ago • Najla Abassi

BATCH.data, var.func=sd, var.cutoff=0.25, filterByQuantile=TRUE) it reduces the total number of genes from 54000 to 10000. Also i get more number of DOWN DEG than UP DEG after performing eBayes. Is there any other simple batch...correction and gene filter package available that didn't interfere with results

DGE limma

updated 7 weeks ago • Amit

gseaParam, : There are ties in the preranked stats (33.92% of the list). The order of those tied genes will be arbitrary, which may produce unexpected results." Does anyone know how to solve this warning as the consistency

fgsea gsea

updated 7 weeks ago • Gordon