Biostar

2,973 results • Page 2 of 60

Dear all, I have a matrix of reads counts for each gene for each strain of an animal. I am using DESeq2 to analyse the clustering of the strains. I have performed a Variance Stabilising Transform on my DESeq2 object and...can do a PCA: p <- DESeq2::plotPCA(vsd, intgroup=c('Condition')) p <- p + labs(title = 'PCA on gene expression levels') p Now, I would like to know the coeffi…

deseq2 pca gene list loadings

updated 7.2 years ago • cristian

Dear all. I am using DESeq2 for analyzing differential expression of DRIP-seq data. About [DRIP-seq][1] data, I have BAM files and BED files.(used featureCounts...I already tried DESeq2 with BAM files, but I heard that BED files can be used in DESeq2.(I am not sure it's true.) Could you tell me how to use BED files...in DESeq2 if I can use BED files for analysis? Thank you! [1]: https:…

R DESeq2 DRIP-seq

updated 4.9 years ago • H.Chloe

counts by the gene length, to end up with RPK (reads per kb). Can this matrix be used as an input to DESeq2 for normalisation and differential abundance analysis? PS. No library size normalisation was done (which I intend...to do using DESeq2

deseq2

updated 7.0 years ago • adityabandla

Dear all, Just a quick clarification about importing pseudocounts into the deseq2 package. I don't usually apply the bootstrapping step with the Kallisto package for deseq2 analysis. My results are...part when the tsv files are then processed by the tximport package for the downstream analysis with deseq2. Thanks

Deseq2

updated 2.6 years ago • Mozart

tx2gene.tsv my question is: which one of these files should be an input for Deseq2 Bioconductor, if I want to analyze it on my own? NOTE: for doing DEseq2 by Differencialabundance/nf-core pipeline, we have

DEseq2

updated 5 months ago • r.shiasi3897

about likely relationship between the `baseMean` and the `mean of normalised counts` measured in DESeq2. Thing is at the beginning of my analysis I use to filter genes with low counts dds[rowSums(counts(dds)>10) >=n despite...be a relationship between those values, I guess? Could it be that they successfully passed the shrinkage due to very high log2foldchange

RNA-Seq maplot

updated 3.9 years ago • Mozart

I want to know how to use htseq-count data for detecting DEGs by DESeq2. We can get gene expression count matrix by htseq-count, and also we can use this output in DESeq2. However, the last 4 rows...counting result. Do everyone remove last 4 rows by themselves in R ? Or are there any functions in DESeq2 to pass the raw result of htseq-count ? So, in conclusion, I want to know how to connect h…

R RNA-Seq next-gen DEG Mapping

updated 4.8 years ago • scheme4193

tutorial as mentioned here to perform single cell analysis: https://github.com/mikelove/zinbwave-deseq2/blob/master/zinbwave-deseq2.knit.md I could not find any documentation indicating how the weights generated by...ZINB-WAVE are actually used in DESeq2. (I am interested in the model used). Can someone explain this to me or point me to the right literature? Any help is appreciated

deseq zinb-wave RNA-Seq rna-seq deseq2

updated 3.2 years ago • prachitipprabhu

other R package that can do GO and/or KEGG Gene set enrichment analysis from counts generated with DESeq2? I have a set of counts generated via DESeq2, with some very nice differential expression analysis. I was thinking of...normalization, as I could then use the GOana package for GO and KEGG analysis. Can that work with DESeq2, or is there a similar package that can use counts generated in D…

R RNA-Seq rna-seq KEGG GO

updated 3.8 years ago • devarts

I ran all my RNA Seq data through galaxy to get FPKM files from original fastq data, but I did bias correction in Cufflinks. However, the DESeq2 manual stresses that you should use raw integer counts, not normalised counts. Does cufflinks normalise the data to...to get FPKM files from original fastq data, but I did bias correction in Cufflinks. However, the DESeq2 manual stresses that you should …

cufflinks deseq2 bias

updated 8.3 years ago • as9309

Hello. I'm trying to analyzing RNA-seq data with DESeq2 to study differencial gene expression. I have SAM and BAM files generated by samtools. How do I insert my files on R to...run DESeq2? Do I use the SAM files, BAM files or sorted BAM files? Thank you in advance

BAM SAMTOOLS DESeq2 SAM

updated 2.5 years ago • Bioinf_Questions

of these tumors within the ever and never smoker groups. In my clinical data sheet I put into DESeq2 I have 2 columns: Smoking - Y or N Type - A, B, or C I encoded this in DESeq2 as: dds <- DESeqDataSetFromMatrix(countData = cts, colData...coldata, design= ~ Type + Smoking) However, I have been asked to do DESeq2 within each subtype and compare the results across the 3. So, do DES…

RNA-Seq

updated 3.2 years ago • a.basitkhan1990

It's really complicated for me to handle three-factors with DESeq2, though many of the posts on Biostars.I think the developer should make it more clear to users. Three factors are temperature...5)water*co2, (6)temperature*water*co2, (7)temperature*water. I have tried a lot with design in Deseq2, like DESeqDataSetFromMatrix(countData = countData,colData = colData,design = ~co2+temperature+water…

deseq2 three factors design

updated 6.4 years ago • marburg2107

Hello everybody! I am trying to install DESeq2 and I keep getting errors. At first I had about 10 errors regarding packages I couldnt install. The main problem of that...From searching I managed to install RCurl but I still get the bellow error. > install('DESeq2', lib = '/home/kostas/R/x86_64-pc-linux-gnu-library/3.6') 'getOption("repos")' replaces Bioconductor standard repo…

DESeq2

updated 2.0 years ago • tsomakiank

to do rna-seq analysis but as i ve read and been told cuffdiff is outdated and now i have been using deseq2 ( i got no idea of R but with the help of this link : https://dwheelerau.com/2014/02/17/how-to-use-deseq2-to-analyse-rnaseq-data...Results from cuffdiff also had basemeanA basemeanB ( two conditions or two samples ) but deseq2 just gives 1. Can someone tell me the code in R to add so i can …

RNA-Seq

updated 6.4 years ago • dimitrischat

I'm having difficulty performing DESeq2 analysis on FeatureCounts data from Galaxy. I've tried [both][1] [these][2] websites, but I can't seem to properly format my...I'm having difficulty performing DESeq2 analysis on FeatureCounts data from Galaxy. I've tried [both][1] [these][2] websites, but I can't seem to properly format my FeatureCounts data for DESeq2. My FeatureCounts output file from Ga…

RNA-Seq

updated 6.3 years ago • Newbieish

I m running Deseq2 pipeline my final result file is like 18,000 genes .So how do take the differential expressed genes from my list of genes...Do i sort if based on p value or is there a way to do inside the deseq2 before getting the final list of genes Any help or suggestion would be appreciated

R RNA-Seq

updated 7.0 years ago • krushnach80

Hello everyone, How does the DESeq2 work? For example, if I have a large number of patients before and after treatment, does DESeq2 compare each patient separately

DESeq2

updated 2.3 years ago • wmsalsah

Help! I'm trying to install DEseq2 to perform differential gene expression analysis R Studio. I'm using the free R Studio on Posit Cloud. R Sudio version...Bioconductor version 3.18 (BiocManager 1.30.22), R 4.3.2 (2023-10-31) BiocManager::install("DESeq2") 'getOption("repos")' replaces Bioconductor standard repositories, see 'help("repositories", package = "BiocManager")' for...latest Bioconduct…

DEseq2

updated 5 months ago • dantuluri

replicate. With two biological replicate. I want to do differential gene expression analysis using DESeq2 so I tried these codes after reading about DESeq2: ,my aim is to do the pairwise comparison. how to make colData and design...formula. library("DESeq2") countMatrix = read.table("read_count.22May.2017.new.txt",header=T,sep='\t',check.names=F) head(countMatrix) …

RNA-Seq

updated 6.9 years ago • Bioinfonext

Dear all, After running DESeq2 program successfully I found out that I had to detect and remove outliers from my htseq count datasets before running...DESeq2. However, I am a little confused about how to perform this task. Can u advise me the most straightforward way to do this

RNA-Seq outliers deseq2

updated 5.8 years ago • nazaninhoseinkhan

to my methods so far, I have run a differential expression analysis of nonmodel organisms using DESeq2. I was able to use the coding sequences (cds) from a genome published on Ensembl as my reference for DESeq2, though the organism...Is there a way I can create a function annotation or discover gene ontology and connect that to my DESeq2 results? I was considering BLASTing the cds fasta, but I am…

RNA-Seq rna-seq gene R

updated 3.1 years ago • snow4964

Hello! I'm working on my DESeq2 data analysis and I want to make a report with R Markdown. But I have a problem when I get to the deseq2 plotMA part. In the

markdown R plot deseq2

updated 2.5 years ago • Pahi

Hi all: I am using sever to analyze RNA-seq data. I am in Anaconda3. Under Anaconda3 I called R, it shows it is R 3.5.1 R version 3.5.3 (2019-03-11) -- "Great Truth" Copyright (C) 2019 The R Foundation for Statistical Computing Platform: x86_64-conda_cos6-linux-gnu (64-bit) Then I tried to install DESeq2 on R following the bioconductor instructions: But I got the error like th…

R RNA-Seq software error rna-seq sequencing

updated 4.0 years ago • Kai_Qi

all human genes in two groups of patients. (each group includes several samples) I am going to use DESeq2 to explore if there is any gene whose expression significantly changes between two groups. DESeq2, however, seems like...accepts only nu-normalized counts for the RNA seq. Is there a way to feed the DESeq2 with RPM data

DESeq2 RPM data

updated 5.1 years ago • ruhollah

Hi all, if you know the full name of `padj` in DESeq2? I know if it corrected p-value, but It should be the abbreviation, so if you know the full name for that

RNA-Seq

updated 4.5 years ago • mxlsherry1992

Hi friends I want to use DESeq2 to normalize the raw count data to do PCA. I dont have colData. What code should I use? because in the DESeq2 workflow we

RNA-Seq

updated 2.3 years ago • Rob

Hi everyone, I use DESeq2 for all of my RNA-Seq analysis. Can anyone recommend a tool that works seamlessly with DESeq2 data to perform enrichment

DESeq2 RNA-Seq RNA-Seq

updated 6.8 years ago • gkuffel22

For RNA-seq data analysis using DESeq2, a recommended method for batch effect removal is to introduce the batch in the design of the experiment as `design...For RNA-seq data analysis using DESeq2, a recommended method for batch effect removal is to introduce the batch in the design of the experiment as `design = ~ batch...For RNA-seq data analysis using DESeq2, a recommended method for batch effe…

Combat DESeq2 Batch-Effect

updated 4 weeks ago • Arindam Ghosh

groups of these patients, in the expression levels of a particular gene (only one!). Could I use DESeq2 to do that? The problem is that I can't use a statistical model directly on the raw data, then I would firstly normalize...the raw data of this gene, secondly I want to do a correct statistical test. I thought to use DEseq2 to normalize my gene using all the 150 genes, then do DESeq2 analysi…

R gene DESeq2 DE

updated 7.9 years ago • fischer87

Hi, For a while now, I've been looking at the intersect of the significant results from DESeq2 and EdgeR as my standard for determining differentially expressed genes, treating EdgeR as a filter over the DESeq2...results. I usually report fold-changes from DESeq2 as the foldchange shrinkage when counts are low or highly variable is nice for not putting too much weight on results

RNA-Seq differential-expression

updated 6.5 years ago • Adamc

model, are they regressed out or just accounted for. Second, why is the nbinomwald test used when in DESeq2 is already is getting you log2 fold changes with p values using DESeq2(dds) which also accounts/regresses out for you...confounders in your model that you put when creating the DESeq2 object. Hope my question was clear and would appreciate any help. Thank you

Seq expression differential RNA

updated 5 months ago • mropri

Hello I am trying to use edgeR's `filterbyExpr` with DESeq2. I am running into an issue where I cannot use `filterByExpr` with DESeq2, unless I do not specify keep.lib.sizes = FALSE

DESeq2 RNA-seq edgeR

updated 14 months ago • biotrekker

How can I extract the normalized and transformed read counts in deseq2 which are used to calculate the log fold change

deseq2 data read counts

updated 4.8 years ago • anna

Hi All, I am plotting PCA via pcaplot in Deseq2. I am interested to look at other pca plots like pca3 vs. pca4 as well. How could I have this information in Deseq2? Thanks

RNA-seq

updated 5.7 years ago • mkh

I'm trying to do differential expression on label imbalanced data; my case:control ratio is 2:1. I know that regressions are at the core of DESeq2 machinery and I know regressions have internal machinery for coping with such imbalances. Specifically, you can down-weight observations from the over-represented group to force an equal contribution to the learning. Is observation weighting available …

deseq2 label-imbalance regression

updated 7.6 years ago • bkellman

novo assembled with Trinity and started using the assembly in a differential expression analysis in DESeq2. However, I also have supertranscripts assembled by Trinity and recently learned about DEXSeq. Would it be redundant

deseq2 dexseq trinity

updated 3.6 years ago • pthom010

hi I am getting error while running deseq2 in usegalaxy. This is the error: > Error in scan(file = file, what = what, sep = sep, quote = quote, dec = dec, : line 2 did not have 14 elements

deseq2 miRNA

updated 4.8 years ago • anjuraas

How can StingTie GTF which contains FPKM values of the transcripts be transported to DESeq2 ? In there any step that has to be incorporated somewhere between StringTie and DESeq2 to make DESeq2 easily read the

Cufflinks DESeq2 RNA-Seq StringTie

updated 2.9 years ago • akashdkyshyap001.ad

I'm trying the tuxedo protocol as well as analysis using DESeq2, I wanted to see if I can see in the difference of DE genes. DESeq2 uses something called count matrix ,which I generated...ht-seq and featurecounts .Now I want to know how do I transform those counts to make it usable for DESeq2 analysis I see the count table from ht-seq and featurecount whats the difference between both the output…

R RNA-Seq

updated 7.2 years ago • krushnach80

Hello, I have 3 tumor samples and 3 control samples (paired) i read that I should use the following design formula for DESeq2: design(dds) <- ~ patient + condition patient: colnames(cts) , and condition: levels normal, tumor (where normal is the base level...samples and 3 control samples (paired) i read that I should use the following design formula for DESeq2: design(dds) &am…

RNA-Seq deseq2

updated 5.8 years ago • Pin.Bioinf

Hi All, I would like to do differential abundance analysis using DESeq2 for shotgun metagenome data. I have used the MOCAT2 for generating functional annotations. Eg: For ARDB database, Do...which didn't get assigned to any of the ARDB categories - which is around 99% of the reads) for DESeq2 analysis? Will "unassigned reads" impact the sizefactorestimation calculation

deseq2 mocat2 metagenomics

updated 4.7 years ago • anjali.kumari

to generate a heat map of the top differentially expressed genes between two samples. I have used DESeq2 to identify these. My code is library(DESeq2) countData = read.csv("data.txt",header = T,sep = "\t") colData = DataFrame(condition

RNA-Seq

updated 6.9 years ago • sumithrasank75

I'm trying to perform a differential gene expression analysis in which I want to compare edgeR and DESeq2 methods. I've already done the stagewise testing for edgeR and was wondering if there's a stagewise testing procedure...for DESeq2, as well? Thank you

R rna-seq next-gen sequencing

updated 3.4 years ago • Jay-Run

Hello, I am currently using DESeq2 for differential gene expression and am confused about prefiltering. First off, I know DESeq2 has Independent filtering...and not the filtered genes? How can I use the counts of the genes for ONLY THE FILTERED GENES that DESeq2 finds using Independent filtering. Also, is it better practice to filter prior to normalizing, or is it better to normalize

DESeq2 RNA-Seq Differential-Gene-Expression

updated 10 months ago • turcoa1

Dear all, From the DESeq2 guide (http://bioconductor.org/packages/release/bioc/vignettes/DESeq2/inst/doc/DESeq2.html#countmat) I try to read...66050 67 59 41 27 54 23 ``` Is casting to as.matrix a must for DESeq2? Could someone advise? Thanks, Gregor

deseq2 R

updated 13 months ago • Gregor Rot

I'm conducting a differential expression analysis using DESeq2. Before running the analysis I removed the lowely expressed genes. In the DESeq2 results I got around 1000 low counts...genes. So, I went back and cleaned the raw data even move. I run DESeq2 again, now the low counts in the results are aroud 600, but the DEGs number also went down. I don't know if there is an answer

DESeq2 r

updated 2.2 years ago • LN12

Hello, the question I have is - log to which base is reported when we use `test.use="DESeq2"` in the `FindMarkers()` function? I know the default logFC while using Wilcoxon test in `FindMarkers()` is reported in the...Hello, the question I have is - log to which base is reported when we use `test.use="DESeq2"` in the `FindMarkers()` function? I know the default logFC while using Wilcoxon test i…

RNA-Seq seurat single-cell DESeq2

updated 4.2 years ago • suvratha

RNAseq raw counts and normal tissue raw counts and rows with Ensembl IDs. I am trying to use the DESeq2 to get fold change between tumor and normal tissue. All of the DESeq tutorials or examples have much more complicated...with data that is structured completely differently. Does anyone have an idea of how I can use DESeq2 to get fold change from my simple matrix

RNA-Seq DESeq2 R

updated 5.9 years ago • tweiskittel94

Hi, I am using DESeq2 for RNA-Seq data. I got 557 genes deferentially expressed with 5% FDR and Log Fold change >= +/- 0. I would like to choose the...top genes that have a fold change >=2. How do I do that in DESeq2? Can I just export the list of 557 genes and filter them by fold change >=2 or do I have to use any argument in the results...function to statistically calcul…

RNA-Seq

updated 6.7 years ago • EpiExplorer

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