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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 4 weeks 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 4 weeks 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 4 weeks 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 4 weeks 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 4 weeks 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 4 weeks 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 4 weeks 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 4 weeks ago • Mozart

before going more into details and I have trouble understanding one thing. After running it on my DESeq2 results utilising the package ClusterProfiler and function gseGO and watching some tutorials about how to do it

GSEA pathways GO-terms

updated 5 weeks ago • Manko47

Dear Community members, I want to conduct a DESeq2 analysis on 20 samples from 11 donors on a data from a longitudinal study regarding exposure to a certain agent. Each

linear-regression paired-analysis DESeq2 longitudinal-analysis

updated 5 weeks ago • IM

vs. HA_uninfected, CA_infected vs. CA_uninfected, and HA_infected vs. CA_infected. Right now, my DESeq2 design is ```design =~ breed + status + breed:status```. First of all, **is this correct**? Also, how do I then do the contrasts? I tried ```res_HA_PBS_vs_Infected

RNA-seq DESeq2

updated 5 weeks ago • AHerik

ko:K21596 Zm00001eb3236400 - Zm00001eb0802600 ko:K10406 Zm00001eb0264900 ko:K13946 ``` My DEGs list (deseq2): ```r baseMean log2FoldChange lfcSE stat pvalue padj Zm00001eb000370 83.58504092 2.580437493 0.33040911 7.809825506

KEGG clusterProfiler Zea-mays

updated 5 weeks ago • sansan_96

Hi, I’m trying to correctly identify some DEGs using DESeq2 in a mini-time series (2 timepoints, early and late infection). Simply grouping everything into one overall “treatment

RNAseq DEG DESeq2

updated 5 weeks ago • ian.will

Hi all, I'm using DESeq2 to normalize my counts dataset which has about 90 samples and 252 taxa. I will need this for WGCNA analyses which I have

DESEQ2 WGCNA

updated 5 weeks ago • DNAngel

I am running DESeq2 to find DEGs between multiple samples, but I'm not able to decide what type of design to use, and how to arrange my data...I am running DESeq2 to find DEGs between multiple samples, but I'm not able to decide what type of design to use, and how to arrange my data? My data the following categories- ---------- **1.DISEASE SUBTYPE | 2. TYPE OF MUTATION** A …

Differential-Gene-Expression RNA-Seq DESeq2 R

updated 5 weeks ago • ginny

After performing DESEQ2 on my data, I could able to plot MA, PCA, and EnhancedVolcano plots including a (.xlsx) file consisting of log fold change...head(countData) metaData <- read.table("phenodata.csv", header = TRUE, sep = ",") head(metaData) #Deseq2 library(DESeq2) dds <- DESeqDataSetFromMatrix(countData=countData, colData=metaData, design=~stage_condition) dds

Differential-gene-expression RNA-Seq

updated 5 weeks ago • Pranathi

Hello, I am doing a RNA-Seq DE analysis with DESeq2 and I was told to not consider the gene basal expression level as 0, so, how would I do that step? Are they referring to the...relevel** function in DESeq2? or setting the control samples as the targets of the comparison? Or is there more to it that i am not aware of? Also, would...results differ a lot if I do the analysis as indicated in th…

DESEQ2 RNA-Seq Differential-gene-Expression

updated 5 weeks ago • Pin.Bioinf

Hello everybody, I am fairly new to the RNA-seq workflow and I am currently struggling how to evaluate the performance of the RNA-seq pipeline I am trying to establish, which will be used to investigate differential gene expression. Lets say I have 3 different pipelines: 1. kallisto -> tximport -> DESeq2 -> 160 differentially expressed genes (random number) 2. …

Differential-gene-expression RNA-Seq R DESeq2

updated 5 weeks ago • nhaus

from Kallisto. Kallisto has output 1) estimated counts, and 2) tpm values. I am hoping to perform DESEQ2 analysis on these data. The DESQ2 documentation suggests that I should be using only count data as input. However, both...continuous real numbers. What is the proper preprocessing to use Kallisto quantification tables on DESEQ2

read-counts DESEQ2 differential-gene-expression kallisto

updated 5 weeks ago • mrj

each with two replicates. My question is what is maximum number of genes that we can enter into a DESeq2 or EdgeR models to get a statistically sound differential expression analysis. Background: the samples contains

Differential-Gene-Expression EdgeR DESeq2

updated 5 weeks ago • rieza.aprianto

I'm getting inconsistent numbers of genes from DESeq2 results. Using the default FDR, On `summary(res)`, I have: ```r out of 26572 with nonzero total read count adjusted p-value &lt...I'm getting inconsistent numbers of genes from DESeq2 results. Using the default FDR, On `summary(res)`, I have: ```r out of 26572 with nonzero total read count adjusted p-value < 0.1

differential-gene-expression RNA-Seq DESeq2

updated 5 weeks ago • Chris Gene

construct my final transcriptome - Quantification using Kallisto - Tximport to could use my data on DESeq2 Are there some important caveats here? Should I work with whole my transcriptome (fresh) instead of process it a little

differential-gene-expression RNA-Seq ORFs

updated 5 weeks ago • pablo61991

I have at hand has ~50 CPU, each with 12 cores and plenty of RAM. I have 1. browsed through the DESeq2 vignettes and I feel it may be a good fit. 2. Removed housekeeping genes, in the hope that it makes the task of the software

differential-gene-expression RNA-Seq GTex DESeq2

updated 5 weeks ago • vikram

my differential gene expression analysis (kallisto to get pseudocounts, tximport to give them to DESeq2, and DESeq2 to test differential expression). Now when I'm trying to work with some of my extremely up-regulated genes

differential-gene-expression RNA-Seq

updated 5 weeks ago • pablo61991

other 50% are false transcript or just unknown transcripts. For example, if my next step is to fed DESeq2 with these counts, I need to use tximport and I need to give to the program the tx2gene file which come from my annotation

differential-gene-expression RNA-seq

updated 5 weeks ago • pablo61991

3) I am also not quite sure what conclusion can be drawn from the MA plot. 4) What is the need for shrinkage? Thank you

differential-gene-expression deseq2

updated 5 weeks ago • sagnik

I am using DESeq2 to find differentially expressed genes between conditions control/treated. The PCA using vst counts shows family

differential-gene-expression RNA-Seq deseq2

updated 5 weeks ago • firestar

I ran DGE on my dataset using DESeq2 and Limma. I used the same dataset, similar settings and same GLM model (`~family+condition`). The number of DEGs I get are...I ran DGE on my dataset using DESeq2 and Limma. I used the same dataset, similar settings and same GLM model (`~family+condition`). The number of DEGs I get are as...0.05 and BH adjusted q-values <0.05 shown separately): ```r To…

limma differential-gene-expression RNA-Seq deseq2

updated 5 weeks ago • firestar

RP23-317L18.3 2233 TEC 2233 2048.998 0 0 ``` I want to do differential gene expression analysis by DESeq2 on this output and on the basis of Gene_id and NumReads columns, I am not sure actually if aggregated gene name based

differential-gene-expression Salmon

updated 5 weeks ago • lkianmehr

R1, and D3 vs R3. what is your suggestion for these samples of first group to do DGE? I did DGE by DESeq2, but its developer would not recommend DESeq2 for such conditions that compare individually and combining samples

Differential-gene-expression RNA-Seq

updated 5 weeks ago • lkianmehr

Trying to analyse count data using R, its throwing error "duplicate 'row.names' are not allowed" . when in reality I have checked the files if there's any discrepancy (as in duplicate row present and whether the sample data matches with count data). Can anyone help? I found this in this blog, someone's comment "From what I've understood from answers to similar questions, a possible problem ma…

RNA-Seq deseq2 Differential-Gene-expression R

updated 5 weeks ago • imanbh

of the genome. I have seen samples which have ~80 million reads, but when looking at count data in DESeq2, the sum of counts for the sample in question only has a count sum of ~3 million. So, I'm curious how to interpret this ~10-20

differential-gene-expression RNA-Seq deseq2

updated 5 weeks ago • contact

Hi Currently I am working on differential gene expression and using DESeq2 package but during execution I got error that expression values should be integer and my expression values in float

differential-gene-expression

updated 5 weeks ago • sana777munquad

library = DBA_LIBSIZE_PEAKREADS) # DBA_LIBSIZE_PEAKREADS for matching results the way DESEQ2 calculate size factor using library size withing the interval obj <- dba.contrast(obj, minMembers = 2,categories...df_diffbind_test_de <- df_diffbind_test_all0.05 %>% dplyr::filter((Fold > 2 | Fold < -2)) # -------DESEq2 ----------- # Get count matrix from Diffbind rat…

diffbind deseq2

updated 5 weeks ago • Ankit

Dear all, I am using DESeq2. My design matrix have two columns: status(1,2), and condition (C1,C2). I am only interest in detecting what genes are D.E. between

interaction LRT deseq2

updated 5 weeks ago • klervi-lugue

I was writing a deseq2 script to analyze wild type p53 and mutant p53 samples, my problem is that my wt sample contains 3 samples with 3,3 and...of samples and replicates for both the conditions or can I somehow use this design too? ```r # Load DESeq2 library library(DESeq2) # Read count data for all samples wt_samples <- c("SRR8435995", "SRR8435996", "SRR8435997", "SRR19…

RNA-seq R DESeq2

updated 5 weeks ago • naveedhasan2000

Hi all, I am working on the DE analysis of primary vs metastasis using a small set of paired-samples (8 primary tumors & 8 metastasis). After Variance stabilizing transformation using DEseq2, my PCA plot shows that the samples group by patient and I cannot really differentiate the Primary to the metastasis groups. As consequence, I cannot find any differentially expressed genes between …

Batch-effect DESeq2 combat_seq

updated 5 weeks ago • l.uva

Hello! Please tell me if my reasoning is correct and how can I do run the proper analysis using DESEq2. I have two batches of RNA-Seq samples: (format: `TYPE_condition_batch`) ``` WT_BASE_batch1 KO_BASE_batch1 WT_LEARN_batch2

RNA-Seq batch-effect DESeq2

updated 5 weeks ago • annamariabugaj

Hello, I'm using this workflow **[DGE analysis using LRT in DESeq2][1]** to look for genes that are significantly differentially expressed over a time-series (2,7,14,53 days) of a RNA-Seq count

KEGGREST DESEQ2 RNA-Seq DEG

updated 5 weeks ago • joana.maclean

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 + condition`. The presence of batch was already known from experiment desig…

Combat DESeq2 Batch-Effect

updated 6 weeks ago • Arindam Ghosh

GSEA using ClusterProfiler with the gseKEGG function. As input data I used a gene list (output from DESeq2, not filtered by fold change or p value) with the KEGG number for each gene and a metric for ranking the genes calculated...with sign(log2foldChange) * -log10(p-value). A) First I used the DESeq2 output from "control vs mutant" data. B) Then I set the contrast for the DESeq2 results at "mu…

ClusterProfiler gseKEGG

updated 6 weeks ago • milkyway

this is ok or just means my normalization was not correct? 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 line and svs as with voom... Or if I am...Thank you in advance!t** ![Example dendrogram with voom][1] ![Example dendrogram with DEseq2][2] [1]: /media/images/1da6819f-8739-47d1-9277-b2009292 […

DEseq2 voom WGCNA

updated 6 weeks ago • gimenagomez

Hello Everyone, I am currently working with bulk RNA seq where I am taking publicly available data and performing DESeq2 on them. For this, I am taking my dataset from GEO and then FTP links published on NCBI SRA. My each file size is between 8...I am currently working with bulk RNA seq where I am taking publicly available data and performing DESeq2 on them. For this, I am taking my dataset…

SRA FTP GEO NCBI

updated 6 weeks ago • Aaliya

I wanted to know how to computationally use TMM normalization (typically used with edgeR) with DESeq2. I've read that it's possible to do so. In my analyses, I've always used tximport initially, DESeq (ddTxi), and then worked on

RNA-seq DESeq2

updated 6 weeks ago • marco.barr

human plasma (4 groups). I have used the miARma-Seq pipeline (http://miarmaseq.idoproteins.com/) and DESEQ2 for the differential expression analysis. We used a spike in control (c. elegans miR 39). Can anyone advise the best method

spike-in miRNA

updated 6 weeks ago • PJC

Hi Kevin, I am trying to plot a volcano plot with my DESeq2 results. I managed to get it working with most of the files, but I cant get rid of the default row numbers and replace it

EnhancedVolcano

updated 6 weeks ago • Mohan

Good evening, I am doing a DE analysis on rna-bulk seq data aligned with salmon (with DESeq2 standard workflow). Recently, I found that, biologically, a particular gene is important/relevant for the analysis...Good evening, I am doing a DE analysis on rna-bulk seq data aligned with salmon (with DESeq2 standard workflow). Recently, I found that, biologically, a particular gene is important/relev…

R salmon DE DESeq2

updated 7 weeks ago • DYLAN NICO

microarray runs. Pretty skeptical about this, but having my RNA sequencing results output from DeSEQ2 and eager to generate some figures for my boss, for us to see what is going on. I try to run the following command, only for

updated 7 weeks ago • aleksk779

files for each sample. To extract the list of Differentially Expressed Genes (DEGs), I used the DESeq2 function in R. I used the abundance.h5 file for analysis. However, I'm not clear on the concept of normalization (I understand...But I'm unsure if that's true. Do I need to perform additional normalization when using DESeq2? The tsv file contains both TPM and est_counts. If using abundance.h5…

RNA-seq normalization DESeq2

updated 7 weeks ago • JH

I am trying to run this analysis, but it generates the warning shown below. Can someone please help me figure out the issue? ```r ddset = DESeqDataSetFromMatrix( countData = counts.matrix, colData = properties2, design = ~Group + (1 | Cell_type) ) Error in checkFullRank(modelMatrix) : the model matrix is not full rank, so the model cannot be fit as specified. Levels or combina…

deseq

updated 7 weeks ago • MAPK2

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