Biostar

2,973 results • Page 1 of 60

I discovered a problem while trying to analyze RNA-seq expression data using DEseq2. DEseq2 is a tool for unnormalized data, that is, raw count, and my data is RPKM data. Since all I have is an expression matrix

DEseq2 RNA-seq

updated 5 hours ago • mnx0723

can anyone suggest me about the results of differential gene expression analysis using DESeq2. i have 10 samples, of which 6 are disease and 4 are healthy, i have find the raw counts and now i have run the following code...t collapse/merge the samples" ![the R script][1] the output results of this is ![output of DESeq2][2] [1]: /media/images/c1611c21-269b-4fb1-a429-6b33adbb [2]: …

differential expression gene rna-seq Deseq2

updated 1 day ago • ahmad.sajad4541

trying to do a differential abundance analysis on some 16S rRNA sequencing data using R package DESeq2 to find differentially abundant taxa among my two study groups. The problem I am having is that I find the same microbial...classifier could achieve better results? I've also read online that some people do not recommend DESeq2 for this type of data and instead suggest other approaches such …

microbiome 16S DESeq2

updated 2 days ago • Antonio

to do this yet, but I want to ask about a further step in the analysis. When comparing tissues in DEseq2, normally we use a control group as a reference. But in this case, I don't have any baseline reference with which I can compare...all tissues. Can I still use DEseq2 for this purpose? If its possible, how exactly? If not, is there any other method you can suggest for me? I'm new to the topic

DEseq2 RNA-seq DEG R

updated 2 days ago • M.

library path and load required libraries .libPaths("/sci/labs/maayan.salton/adi8897/R_libs") library(DESeq2) # Define the full paths to your count files for the first analysis (Israeli_WBP4_mutant) countFiles <- c( "SRR9600556_sorted_counts.txt...y) merge(x, y, by = "gene", all = TRUE), countDataList) # Convert merged data frame to a matrix for DESeq2, with genes as rows and samples as…

DESEQ2 logfoldchange

updated 4 days ago • adi.gershon1

Please help me anyone. I have done everything to solve this problem but didn’t get any solution. I am doing differential expression analysis using DESeq2 package of R. Everything is looking okay in my input files. I checked many times, the rownames in sample info file are equal...to solve this problem but didn’t get any solution. I am doing differential expression analysis using DESeq2 package of…

deseq2 R

updated 5 days ago • Erina

normalisation methods are not preferred choices and often raw counts are used directly as inputs for DESeq2 or EdgeR normalisation. I did some further reading on DESeq2 and EdgeR normalisation methods, but they use the label

rna-seq

updated 6 days ago • Yuju

Hello. Since I'm not from an English-speaking country, please excuse my lack of proficiency in English. I'm currently conducting RNA-seq analysis. I used kallisto for mapping and quantification, and obtained counts. The experiment was performed with biological triplicates for both wild-type and mutant samples. I normalized using DESeq2 and obtained a list of differentially expressed genes. Howev…

RNA-seq TPM Normalization DESeq2

updated 6 days ago • JH

Hello to all biostars, For months I have managed to do this with expression patterns and now I have to interpret it, but it generates doubts and I really want to interpret it in the best way, or be as accurate as possible. My data are from stages of cell development, and what we are looking for is the relationship between the different stages and the unique patterns that these genes show, of co…

RNA-seq ontology GO

updated 6 days ago • Oscar

Dataset of which I did mapping, and filtered out the genes, and then put it as an expression data in DESeq2, these are some problems I would like to address. when I put in the dataset, I am not able to run it for DEG analysis because

deseq2 R

updated 7 days ago • jagdish7921

seq data analysis. I was wondering if anyone can send me a link or paper to better understand how Deseq2 works

Deseq2

updated 8 days ago • Sudip

I have 2 factors in the design formula in DESeq2 dds <- DESeqDataSetFromMatrix(countData=count_data, colData=coldata, design=~condition+timepoint) but got an error...Please read the vignette section 'Model matrix not full rank': vignette('DESeq2') This is what my coldata looks like: condition timepoint HA Healthy 0dpi HB Healthy 0dpi HC Health…

RNA-Seq DESeq2

updated 9 days ago • DOBI

any other statistical tool that can take in my 4 WT studies and 4 Mutant studies? Each study has a DESeq2 output generated. Thank you

DESeq2 PCAplot

updated 13 days ago • Aaliya

I generated TPM for the RNAseq data that am dealing with ,as the samples that i have pooled for my project are from different experiments and my requirement is to get genes exclusive to one condition irrespective of high/low expresion, i generated TPM from RSEM tool, the RSEM output didn't give any p-value as oppposed to what was mentioned in their manual. I need p-values . I understood that feed…

P-value TPM RSEM

updated 14 days ago • VITALA

I have 8 samples (4 WT and 4 mutants). I have performed bulk RNA seq on these (Kallisto, and then DESeq2) I am attaching my PCA plot, I was expecting the wild type to cluster together and all the mutants to be together, but this

DESeq2 PCAplot

updated 14 days ago • Aaliya

sample/samples vs the epithelial cells of a treatment sample/samples. I know I can run edgeR or DESeq2 for differential expression for full genes but would a wilcox test also work, especially if I want to test the difference

scRNAseq

updated 14 days ago • mropri

down") Now, i'm in need of help to find the most similarly expressed genes. Based on my research DeSeq2 have a section/scripts that allows users to extract result table from DGE with alternatives hypothesis using 'results...lt; x. As shown in the link below https://www.bioconductor.org/packages/devel/bioc/vignettes/DESeq2/inst/doc/DESeq2.html#tests-of-log2-fold-change-above-or-below-a-thresho…

NOIseq

updated 15 days ago • alifafiq1

Hello, I have a raw count matrix and I did some analysis with DESeq2 but now I want a TPM normalized matrix for CIBERSORTx. I have the fastq files and I read some post that say that I have...Hello, I have a raw count matrix and I did some analysis with DESeq2 but now I want a TPM normalized matrix for CIBERSORTx. I have the fastq files and I read some post that say that I have to

tpm row-count normalization

updated 15 days ago • michelafrancesconi9

I used the stringtie -e -B command and received a file like the one attached to this post ![enter image description here][1] When using it in R, I received an output saying that I needed a .ctab file. I tried using the cufflinks environment with the tablemaker command but it said that there was no such command. I really appreciate any advice! [1]: /media/images/25fcc2b8-00bc-4898-99…

Stringtie Cufflinks Ballgown DESeq2

updated 18 days ago • Nina

repos = "https://cloud.r-project.org") BiocManager::version() # Verify version BiocManager::install("DESeq2") # install a bioconductor package ### Switch to the other of the 2 releases for the R version currently running: BiocManager

R Ubuntu Linux Bioconductor Rstudio

updated 19 days ago • BioinfGuru

batch done by different people over different times so I believe we have batch effect. As I am using DESeq2 for my analysis I set my model design as “Batch+Type”. I used removeBatchEffect from limma package and plotted PCA &amp...model design as "~Batch+Type" I really appreciate if you give me some insight, Thanks in advance, **DESeq2** ```r ddsMat.pre<- DESeqDataSetFromMatrix(seM…

Batch-effect RNA-Seq R DESeq2

updated 20 days ago • gokce.ouz

good tool to apply on RSEM values to remove the batch effect? 2. Obtain the htseq raw counts and use Deseq2 to perform the differential expression analysis. I saw previously another discussion about about justifying the...batch effect by adding the 'batch' in the 'design' [design ~ batch+treatment] parameter in Deseq2. Besides this, can anyone kindly provide another good way to remove the batch e…

RNA-Seq batch-effect

updated 20 days ago • Tenghui Chen

and negative values. Since softwares usually require raw count data for differential expression (Deseq2 for example) I am looking for a way to perform the analysis after the integration and correction for batch effect. Do

single-cell Batch-effect RNA-Seq Scran

updated 20 days ago • baldissera152

of allowing a 'corrected' dataset to be assessed using PCA, clustering. Is there any way (e.g. in DESeq2, edgeR or Limma) to do a similar assessment of batch correction sucess using the single-step method? Thanks in advance

Combat RNA-Seq Limma DESeq2 batch-effect

updated 20 days ago • borkk

Hi everyone, I need a help. I have RNA seq data from multiple labs which I downloaded and processed by myself. I created a featurecounts matrix. Now I have two queries: 1. Do I need to remove batch effects? If yes can Deseq2 design matrix (~batch +condition) will be sufficient? Or I need to separately do batch removal (eg. I also tried Combat)? 2. After...a featurecounts matrix. Now I have …

clustering dendrogram RNA-Seq batch-effect

updated 20 days ago • Ankit

1. Calculate the batch factors using **DASC** 2. Use batch factor as a covariate in your **DESeq2** model **Manuscript** is under preparation; will be out soon with all the comparisons to existing methods/tools (& with

RNA-Seq scRNA-Seq R Batch-Effect

updated 20 days ago • Ar

for the batch effect and in my case normalized with TMM) in a program such as EdgeR, limma or DESeq2 to find differentially expressed genes (NOISeq returns a lot of DEGs), but EdgeR and DESeq only can be input with unnormalized

Batch-effect RNA-Seq ARSyNseq limma NOISeq

updated 20 days ago • endikavarela

and lane6 of each sample always cluster together. I guess the batch effect is minimal? I read the DESeq2 work flow. https://www.bioconductor.org/help/workflows/rnaseqGene/#removing-hidden-batch-effects How can I visualized...DE genes)? Is there a more elaborative instruction somewhere including visualization? The DESeq2 design I used is ```r design = ~ genotype + inoculation + genotype:inocul…

RNA-Seq batch-effect DESeq2 Salmon

updated 20 days ago • georgewwp

Dear All, For Deseq2, should I use feature counts files as input (treated vs control)? Should I include the Annotation.gff3 file as well, which

RNA-seq DESeq2

updated 20 days ago • rrehimi

can infer the batch effect based on these negative controls, and account for it in down-stream `DESeq2`analysis. I'd appreciate if anyone can comment whether this approach is reasonable and I if anyone had a similar situation

RUVseq RNA-Seq batch-effect DESeq2

updated 21 days ago • grant.hovhannisyan

Hello there, hope all of you are fine. I do hope you are enjoying this weekend. In my little experience, I always had to deal with samples coming from different batches (i.e. coming from different hospitals or experiments done in different days). One postdoc in my lab showed me how to deal with batch effect by using **SVA package.** I guess it is a brilliant idea to work with that, but if I don'…

RNA-Seq deseq2 batch-effect

updated 21 days ago • Mozart

negative values for count data, which doesn't make any sense. Because there is no DE question, using DESeq2 doesn't make a lot of sense to me (unless DESeq2 can somehow export a TPM or count matrix with batch effect corrected) #### Discussion

gene-expression TPM RNA-Seq counts batch-effect

updated 21 days ago • Ram

I used DESeq2 to process RNA-seq data from different sources. And I found harsh batch effect when plotted PCA (different shapes of

RNA-Seq batch-effect

updated 21 days ago • Rimma

I am currently working on a ChIP-seq experiment with a collaborator and I'm running into problems that may be due to the overall experimental design. So for an overall background, I was brought on as a bioinformatics analyst after the experiment was ordered and sequenced. From what I know so far there were four experimental groups and two replicates for each experimental group. The lab did not …

ChIP-Seq batch-effect sequencing

updated 21 days ago • dmj6ab

variable would explain a big part of the variation in the data, could I model the design in DESeq2 only as a function of it? without modelling for any batch variable? ```r ddsHTSeq3 <- DESeqDataSetFromHTSeqCount(sampleTable

RNA-Seq batch-effect DESeq2

updated 21 days ago • baldissera152

set of DEGs across tissues. Question: Can I treat "tissue" as a covariate? That is, try to get DESeq2/EdgeR to treat it as a batch effect and reduce the effect of the difference between tissues so that I can get an overall

RNA-seq EdgeR DEGs DESeq2

updated 21 days ago • BioinfGuru

counts=counts), colData=colData) dds <- deAna(se0, de.method="DESeq2

RNA-Seq R EnrichmentBrowser

updated 21 days ago • yxswhx

HTseq-count to get the read counts and was able to pick the differentially expressed genes using DEseq2 R package. My DEseq2 output files (Day1 vs Day3) and (Day1 vs Day7) where Day1 is taken as control and Day 3 and Day 7 is taken

RNA-Seq gene-expression-matrix correlation R

updated 21 days ago • aiswaryabioinfo

RNA-Seq WGCNA removeBatchEffect DESeq2

updated 21 days ago • gokce.ouz

Hi, I was wondering if I could get some advice on controlling for random effects using DESeq2. For example, given simulated data: ```r Treatment Batch Estrus Control 1 1 Control 2 2 Control 3 1 Control 4 1 Control 1 2...Hi, I was wondering if I could get some advice on controlling for random effects using DESeq2. For example, giv…

random-effects RNA-Seq batch-effect

updated 21 days ago • Dipro

J 2 IonXpress_RNA_028 Treated J 2 ``` I tried to analyze the data using DESeq2. I checked to see if the samples cluster based on batch and yes, the PCA plot clearly showed two distinct clusters - batch...analysis have got validated in RT-PCR. I understand that the input data has to be raw counts for DESeq2 but is there a way that I can do a differential expression analysi…

Batch-effect DESeq2 miRNA-Seq

updated 21 days ago • prekrish

1,2,3,1,2,3). Is it even possible to account for batch effects for this comparison using edgeR or DESeq2? Or should I just go forward with a typical DE analysis without worrying about batch effects. Thank you

RNA-Seq edgeR DESeq2 Batch-Effect

updated 21 days ago • Behram Radmanesh

I have a RNA-Seq data set (normalized using the DESeq2 library normalization method) consisting 4200 genes and of samples from 22 different species. For each species I...I have a RNA-Seq data set (normalized using the DESeq2 library normalization method) consisting 4200 genes and of samples from 22 different species. For each species I have

RNA-Seq Cross-Species SVA ComBat Batch-Effect

updated 21 days ago • rodguinea

and barch details coldata <- read.table("sample_info.txt", header=TRUE, row.names=1) #Create a DESeq2 object named dds from the gene read count and sample information dds <- DESeqDataSetFromMatrix(countData = cts, colData

sva combat batch-effect DESeq2

updated 21 days ago • svp

matched-normal samples from the TCGA (breast cancer). Following differential gene expression using DESeq2 (design : ~ patient + sample_type), I visualised the differences between sample types (tumour / matched-normal) with a heatmap...effect of patient was perhaps not being accounted for effectively by the design formula I used for DESeq2, so I tried removing patient as a batch effect first with …

ComBat_seq DESeq2 batch-Effect

updated 21 days ago • Mia

datasets by merging the raw counts and then doing the normalization and vst transformation using DESeq2. The plot shows that the samples representing conditions A and B from a dataset are grouping (less separated) together...1, 2, and 3? If I do have to do the batch correction, do I compare different batch effect methods (DESeq2/limma, SVA, Combat-seq)? Do these methods give similar results and…

batch batch-effect DESeq2 rna-seq

updated 21 days ago • mmitra

step would be to normalize the training and test count matrix separately and independently using DESeq2. Will that be OK? I know for scaling the data the mean from the training set should be used for the test set. Is there something...like that we need to be do for the DESeq2 normalization? I mean normalization of the test set based on some parameters from the training set normalization

RNA-seq batch-effect normalization

updated 21 days ago • mmitra

I am trying to run edgeR/Deseq2 using kallisto quant file in galaxy, however i am unable to run it i am having an error in read.table(file = file, header

r edger

updated 22 days ago • Ravita

to control, right? How would you proceed and how would you create the model matrix? I checked the DESeq2 vignette and more specifically the "Group-specific condition effects, individuals nested within groups" section

deseq2 batch-effect

updated 23 days ago • Mozart

So that's the hard bit for a lay person... So once you have your 'dds' object (I am using DESeq2), design formula (es. `~condition`), Limma's function adds the batch object just created and then it fits a linear model for

limma RNA-Seq batch-effect

updated 23 days ago • Mozart

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