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2,981 results • Page 3 of 60

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

Hi, guys. I have a question analysing RNA-seq data(I'm using DESeq2) I'm willing to use **8 samples with high sequencing depth**, and **6 samples with low sequencing depth**.(About 4times lower...Hi, guys. I have a question analysing RNA-seq data(I'm using DESeq2) I'm willing to use **8 samples with high sequencing depth**, and **6 samples with low sequencing depth**.(About 4times lower). C…

deseq2 RNA-Seq sequencing depth DEG

updated 5.6 years ago • woongjaej

Hi I am trying to draw a PCA plot with DESeq2 but somehow I cannot use DESeq2 functions. It is a really simple code i wil be pasting below. > transform <- DESeq2::rlog...an inherited method for function ‘sizeFactors’ for signature ‘"spec_tbl_df"’ > DESeq2::plotPCA(eliminated_data, + intgroup = c('WT', 'Resistant'), …

deseq2 rna-seq

updated 2.1 years ago • edus_bioinfo

Dear all, I am kind of new to DESEQ2 and I have an expression matrix csv that is consisted of ensemble transcription IDs (not gene ids) and their expression...value in each condition. I am wondering if I can use this matrix directly as an input in the deseq2 pipeline. Thanks Cheers

RNA-Seq DESEQ2 R DEG

updated 5.7 years ago • Duckula

I tried to install DESeq2, edgeR and others wilth Anaconda in ubuntu machine with the code: conda install wget samtools r-essentials bioconductor...deseq2 bioconductor-edger as suggested [here][1]. It gave the error Error: Packages missing in current linux-64 channels: - samtools...r-essentials - bioconductor-deseq2 - bioconductor-edger Did you mean one o…

Anaconda DESeq2 edgeR

updated 6.6 years ago • salamandra

The results of RSEM are expected counts of transcripts and genes and they are not integer. DESeq2, however, need a matrix of integer as input. The manual of RSEM said the results of RSEM can be used by DESeq. So my question...is how to import non-integer RSEM counts to DESeq2 for downstream differential analysis? Thank you

rsem deseq2

updated 4.2 years ago • 402374688

about the experiment can be found on bioconductor page below: [Bioconductor post][1] The author of DESeq2 mentioned that I cannot get analysis results for interaction between type and time due to the number of samples. Since...results from GFOLD for differential expression between type and time interaction alongside with DESeq2 results? Thank you. [1]: https://support.bioconductor.org/p/1…

RNA-Seq deseq2 gfold

updated 5.6 years ago • newbio17

matrices in the datasets, it is a raw data and need preprocessing. Can anyone help me how to use DESeq2 libary to preprocess the GEO dataset for Differential gene expression analysis

rna-seq GEO R deseq2 preprocessing

updated 3.9 years ago • hariprasadp.iitkgp

For RNA-Seq DGE analysis using DESeq2, if I have a factor with let's say 5 levels: ```r condition A A B B C C D D E E ``` The standard workflow ```r d <- DESeqDataSetFromMatrix...countData=counts,colData=meta,design=as.formula(~condition)) d <- DESeq2::estimateSizeFactors(d,type="ratio") d <- DESeq2::estimateDispersions(d) d1 <- nbinomWaldTest(d) resultsNames(d1) ``…

differential-gene-expression RNA-Seq DESeq2

updated 3 months ago • firestar

Hello, So I've used salmon to extract readcount and use tximport to be used in DESeq2. After I perform DE analysis, there are some genes that has NA result. I suspects that this is caused by low count or maybe...Hello, So I've used salmon to extract readcount and use tximport to be used in DESeq2. After I perform DE analysis, there are some genes that has NA result. I suspects that this is caus…

deseq2 RNA-Seq

updated 5.5 years ago • bharata1803

sample(9 control,10 cancer)with csv format that merge them with tximport and now want to perform DESeq2 analysis for my merged data to find what transcripts has diffrent expression in cancer and control my sample_key...read.csv, abundanceCol = "TPM") >Key_file=read.csv("Sample-key.csv") >library("DESeq2") but i don't know how to design condition and how to creat countdata …

RNA-Seq

updated 4.5 years ago • z.ghseminezhad92

to generate the raw read count data for my rna seq data. I then used it as an input file in deseq2 to get my differential expression results between the patients and controls . Im wondering why the read count of deSeq2...for one of the genes Im looking at . On FeatureCount I get a read count of around 2000 but for Deseq2 I get a read count of around 4000

deseq2 FeatureCount RNA-Seq

updated 4.5 years ago • Adeler001

with control and treatment conditions. I would like to do differential expression analysis via DeSeq2 to understand how healthy vs. disease state affects the differential expression of genes between the control and...same between each control and treatment condition pair. I have successfully figured out how to use Deseq2 for a simple analysis (eg just looking at how disease/healthy affect di…

rna-seq deseq2

updated 6.0 years ago • jillianrjaycox

Hello, I performed patch-seq for 2 sets of neurons and then used DESeq2 to look for transcriptomic differences between the groups. One group consists of 7 neurons and the second group consists...dataset. I notice that for some genes which are visibly different are not picked as DE genes by DESeq2. A plausible reason for this is DESeq2 is treating the zero counts as dropouts. So, if I added …

patch-seq RNA-Seq DESeq2 Dropouts

updated 2.8 years ago • pkallurkar

in the abundance estimate. If I use tximport to import this abundance information for use in deseq2, is the variance information from bootstrapping used by deseq in any way or does deseq calculate the variance in a...the inferential replicates in to one variance value per transcript. But is this information used by DeSeq2 in anyway during the diff expression analysis? Also, does RSEM perform any…

RNA-Seq kallisto deseq2 tximport

updated 4.1 years ago • divya.nandakumar

I want to use DESeq2 to compare between samples before treatment and after treatment individually as paired samples. For example Pt.1...I want to use DESeq2 to compare between samples before treatment and after treatment individually as paired samples. For example Pt.1 before vs Pt.1 after Pt.2 before vs Pt.2 after Pt.3 before vs Pt.3 after … But I’m not sure if the DESeq2 compares pa…

DESeq2

updated 2.3 years ago • wmsalsah

I am doing DE analysis using deseq2 and I noticed that the threshold of 'low count' changes when I have different inputs. Here' re my questions: 1. How does deseq2...I am doing DE analysis using deseq2 and I noticed that the threshold of 'low count' changes when I have different inputs. Here' re my questions: 1. How does deseq2 determine the low count threshold based on the raw count matrix? I …

RNA-Seq R gene deseq2

updated 4.0 years ago • tianshenbio

I have a question about how DEseq2 handles batch effects/ multiple factors. This is covered in the manual, but I just want to be certain I am doing it correctly...I have a question about how DEseq2 handles batch effects/ multiple factors. This is covered in the manual, but I just want to be certain I am doing it correctly. Say I have an experiment with this design: Sample Age Sex 1 Yo…

deseq2

updated 6.0 years ago • DVA

Hi everyone, I am new in bioinformatics and when I try to use DESeq2 for my counts and further downstream analysis, I am faced with this problem. ```r dds <- DESeqDataSetFromMatrix(countData

RNA-seq subread differential-expression deseq2

updated 8 months ago • Beyza

currently trying to create pseudo-bulk data from single cell RNA data and perform DE analysis using DESeq2. dds_Bcell <- DESeq(dds_Bcell) When I run the above code, the following error occurs: The following error occurred in...cell RNA data. How can I run the DESeq() function when there is 1 sample for each group? Or is DESeq2 analysis not possible in this case? Thank y…

DESeq2

updated 9 days ago • sooni

Hi all, I have raw read counts [of rna-seq]. I need to normalize this data and have done it using DESeq2. But, I found that DESeq2 eliminates the read counts of genes when it's equal to 0. I don't want to lose this data as it might

deseq2 normalization

updated 2.7 years ago • Sandhiya

Hi, I would like to annotate the DE results obtained from DESeq2 with go terms, and then subset by a particular term I am interested in (in this case lipid metabolism). I am using AnnotationDbi...the associated go term? Additionally, I would like to annotate the normalized counts obtained from DESeq2, but this does not work with the mapIDs function in AnnotationDbi, is there a workaround for th…

deseq2 DE R RNA-Seq bioconductor

updated 4.4 years ago • adam.sorbie

Hello, I am a complete novice in regards to utilizing DESeq2. I was wondering if there was anyway to extract data from various GSEXXXXX RNA-Seq specific experiments in order to...perform DESeq2 analysis on them. Right now I have a list of various GSE experiment numbers that are all RNA-seq specific. How would I...about using this list of GSE experiment numbers to be able to prepare the data for D…

GEO DESEQ2 RNA-Seq

updated 3.8 years ago • thewisechineseguru

Hello friends, Based on this post [Question: Differential gene expression based on read counts using DESeq package][1]. Using htseq_count, I generated the raw read count for each gene for my cancer and normal sample. Then I used DESeq and DESeq2 package to identify differential gene expression. 1) First 4 rows are from DESeq output 2) Next 4 rows are from DESeq 2...I generated the raw read c…

RNA-Seq

updated 7.6 years ago • bioinforesearchquestions

I'm noticing that there is a huge difference in the number of diff binding sites found by edgeR and Deseq2. I'm using the default options in dba.analize, just putting the object that I want to analyze and setting method=DBA_ALL_METHODS...For example in a case edge finds 10397 peaks while deseq2 just 1. It's not always the same. Sometimes deseq2 finds more peaks than edge. How can I choose the …

ChIP-Seq

updated 4.2 years ago • francesca3

Hello, If someone can help I will be very grateful. My question is about which design should have my data to run deseq2 and see some comparisons. First, I have the following data: 2genotypes, 2 tissue, and a treatment evaluated in 4 different times (control, t1, t2 and t3). In a matrix it is like this: - library genotype tissue treatment replicate - 1 A …

deseq2 RNA-Seq normalization next-gen

updated 3.9 years ago • LatifaP

Hello! I am doing DESeq2 for the first time. A bit of background: I am downloading the already public data available from ENA browser. I have been...Hello! I am doing DESeq2 for the first time. A bit of background: I am downloading the already public data available from ENA browser. I have been able to successfully do Kallisto on the paired reads. The output of such files in in .tsv for…

Unfolded Kallisto DESeq2 Reponse Protein

updated 3 months ago • Aaliya

Hi everyone, I'm trying to analyze my counts data with DESeq2 and based on the tutorial of GSEA, DESeq2 has an output format that can be used directly in the GSEA ([here][1]). However, I'm reading

GSEA gct DESeq2

updated 2.9 years ago • jabbari.parnian

Hi, all! When I used DESeq2 to analyse the different expression genes, I was confused about two parameters of estimateDispersions, that is sharingMode...and fitType. The DESeq used 'sharingMode="fit-only",fitType="local"' as the default, however the DESeq2 set 'sharingMode="maximum",fitType="parametric"' as the default. How could I select these two parameters? Could I change

rna-seq

updated 8.1 years ago • hellosky2008

are being differentially expressed in the disease case. For genes, doing this is pretty easy with DESeq2. But a collaborator told me that DESeq2 couldn't be used right away for the non-coding transcripts. Is this true? What are...some of the things that I should keep in mind while analyzing non-coding transcripts using DESeq2? He had mentioned that since the amount of ncRNA varies from sample t…

RNA-Seq DESeq2 noncoding

updated 4.2 years ago • c_u

Hi, I am doing differential gene expression by Deseq2 tool. I have no replicates and I am doing multi group comparison between samples. Can anyone tell me how to run the Deseq2

RNA-Seq rna-seq Deseq2 Bioconductor R

updated 3.4 years ago • fatimarasool135

Hi, I have a couple of questions about DESeq2: 1. in the DESeq2 workflow, to test the dex treatment effect, the following command was used: ``` dds <- DESeqDataSet(se, design

RNA-Seq

updated 5.7 years ago • tony.fox2016

My pipeline so far is ```hisat2->featureCounts->DESeq2```. I have generated heatmaps after rlog and log2 transformation of the genes with the most variance, which is somewhat...sample and take the genes with the most log fold change in either direction. I've read through the DESeq2 vignette and haven't found a good example of that. Maybe I do this under the ```design``` parameter…

deseq2 edger RNA-Seq

updated 4.7 years ago • gabriel.jabud

How are outliers determined in DEseq2? I have aligned my samples using STAR and did differential expression analysis with DEseq2. In the output there are

RNA-Seq DEseq2 STAR

updated 3.3 years ago • john.perish

Hello everyone, I have 4 peaks bed files and i want to create count matrix for analysis in deseq2 I want to see the difference acetylation between them, I want in the column the 4 samples, and in the rows peaks I understand

countMatrix deseq2 Chipseq

updated 14 months ago • Chava-Lea

Y and samples also from France with the condition Y. If I want to do the DEG analysis using the DESEQ2 package to know the DE genes between the condition X and the condition Y, how do I have to normalice for the geographical

RNA-Seq deseq2

updated 5.3 years ago • Teresa

Hi, I have normalized count data from RNA-seq protocol. The normalization steps include DESeq2 with design ~1. Unfortunately, I do not have the raw counts. Can I use those normalized counts for DESeq2 with different

DESeq2 log2foldchange

updated 11 months ago • t.ru

Hi all, I want to import salmon transcript estimate output fiels into DESeq2 using tximport. But I have a question. The output of salmon is in TPM But the DESeq2 needs raw data. Is my understanding

into outputs DESeq2 Import tximport using Salmon

updated 2.4 years ago • kimmitzka

Could someone help me understand why my MA plot from DEseq2 has this line of points close to zero, and a second line at about 1.2? I checked the genes from my count table corresponding...Thus I would really like to know what is going on mathematically. Could someone detail how exactly DEseq2 does normalization and obtains the log fold change? Thank you all for your help. ![MA plot][1] [1]:…

deseq2

updated 6.0 years ago • DVA

hi all i am working in RNA-seq dataset in gastric cancer. i am doing differential expression using DeSeq2 in usegalaxy. While doing i am getting this error ![DeSeq2][1] [1]: https://img.techpowerup.org/191203/deseq2.png how can i

RNA-Seq DeSeq2

updated 4.4 years ago • anjuraas

Hi everyone, I have a problem to represent my RNAseq data. I have a list of DE genes as output of DEseq2. So I would like to make an heatmap of these genes across all my conditions (3 conditions, and 3 samples per condition...Hi everyone, I have a problem to represent my RNAseq data. I have a list of DE genes as output of DEseq2. So I would like to make an heatmap of these genes across all my c…

RNA-Seq DEseq2

updated 7.5 years ago • nicolas.hipp

Hi, I have normalized counts data and DESeq2 result file (including log2FC and Padj values) of each sample. And I want to generate a heatmap of significantly differentially...expressed genes from only these files and unfortunately, I do not have the chance to re-run the DEseq2 analysis. Can anyone give me some suggestions on data filtering and scaling options to generate heatmap? From the...DES…

RNA-Seq heatmap DESeq2

updated 4.5 years ago • dnzkursun

I am doing a pre-filtering of my counts following deseq2 vignette: > https://bioconductor.org/packages/devel/bioc/vignettes/DESeq2/inst/doc/DESeq2.html#pre-filtering In

R DESeq2

updated 8 months ago • dylannicoembros

sampe5 N sampe6 N sampe7 N (T:tumor, N:normal) When I use this condition in DEseq2, it will use N vs T as default. If I set `group <- factor(c(1,1,2,1,2,2,2))` in EdgeR. It will get opposite result to DEseq2. I would like

RNA-Seq R EdgeR DEseq2

updated 4.1 years ago • deb0612

Hello, I am using the latest version of Bioconductor 13.6, R 4.2.1 (R console). I managed to install BiocManager, but when I try to install DESeq2, it shows at the end: Warning messages: 1: package(s) not installed when version(s) same as or greater than current; use `force = TRUE` to re-install: 'DESeq2' 2: In install.packages(update[instlib == l, "Package"], l, repos = repos,…

R DESeq2

updated 18 months ago • Artjola

groups of patients I want to normalize this matrix in a way getting TMM or geometric mean values by DESeq2 how can I do that

R RNA-Seq

updated 3.8 years ago • A

is better (or if one of this method is wrong ) for plotting in a heatmap normalised count from deseq2 : `counts(dds,normalized=TRUE)` : z-score( log2(norm count +1) ), z-score(norm count ) or just log2(norm count +1

deseq2 heatmap

updated 5.7 years ago • ZheFrench

Load the DESeq2 library library(DESeq2) # Read your count data counts <- read.csv("C:/Users/anant/OneDrive/Documents/RNASeq/count_data.csv

NGS

updated 11 weeks ago • ananta.kapoor

Hello everyone, Thank you in advance for your feedback and suggestions. I am currently doing some RNA-Seq analysis using DESeq2 and I have noticed that when I plot a histogram of my raw pvalues, I notice most of the genes are at p value of 1. My histogram looks very similar to scenario D of the following link http://varianceexplained.org/statistics/interpreting-pvalue-histogram/. My first ques…

RNA-Seq DESeq2 R

updated 5.5 years ago • lisa.k.mills87

start a new question. I have analysed the same data now both with the two-step normalization using DESeq2 but also with the [erccdashboard][1] package. In the DESeq analysis I have got almost 400 genes with an adjusted` p-value...with log2FC>0 are !='NA' in the results list. All the other genes are NA). If I am doing the DESeq2 analysis without the independent filtering (by setting it i…

deseq2 normalisation quasiseq erccdashboard

updated 16 months ago • Assa Yeroslaviz

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