Showing : DeSeq2 • reset
3
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DESeq2: Design model includes sex but only one female
DESeq2
updated 2.1 years ago by 43k • written 2.1 years ago by • 0
0
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1
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1.7k
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DeSeq2 normalization 16S
DESeq2
updated 2.1 years ago by 43k • written 2.1 years ago by • 0
0
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4
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1.5k
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DESeq2 : standardising variation between treatments
RNA-seq DESeq2
2.2 years ago • updated 2.1 years ago ar14g12 • 0
0
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2
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863
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Issues with ddseq2 for treatment response factoring in different KO clones
Clonality RNASeq DESeq2
updated 2.2 years ago by ★ 1.4k • written 2.2 years ago by • 0
0
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1
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917
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DeSeq2 data comparison and extracting outputs
DESeq2
updated 2.2 years ago by ★ 1.4k • written 2.2 years ago by • 0
1
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5
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1.6k
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Mixed up sample info with plotPCA
plotMA ggplot2 plotPCA DESeq2
updated 2.2 years ago by 43k • written 2.2 years ago by • 0
0
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4
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1.1k
views
Extract LRT results for each comparison
LRT DESeq2
updated 2.2 years ago by ★ 5.0k • written 2.2 years ago by • 0
2
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4
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1.6k
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Deseq2 calculated log2foldchange not consistent with RPM in IP-small RNA-seq
RNASeqData DifferentialExpression SmallRNAData DESeq2
2.2 years ago Shihui • 0
0
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5
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1.1k
views
DESeq2, results(dds, name = <reference>) interpretation results
DESeq2
2.2 years ago Rockbar • 0
0
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3
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1.0k
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Deseq2, multifactor model design for comparing adult Mutant mouse versus pup Mutant mouse with normalization to the age difference of the Wildtype co…
DGE DESeq2
2.2 years ago ruba-mahmoud • 0
0
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5
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1.2k
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DeSeq2 design fails (full model matrix is less than full rank)
DESeq2
updated 2.2 years ago by 68k • written 2.2 years ago by ▴ 10
1
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3
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2.5k
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How does DESeq2 calculate FPKM values when gene lengths are not supplied?
deseq2
written 5.7 years ago by • 0
0
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4
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1.5k
views
filtering out lowly expressed genes by groups
RNASeqData DESeq2
updated 2.2 years ago by 68k • written 2.2 years ago by ▴ 10
1
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3
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1.5k
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Deseq2, enrichGO and ensembl ID
go DESeq2
updated 10 months ago by 68k • written 2.2 years ago by • 0
0
votes
3
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899
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how to adjust other conditions when calling DEGs by DESeq2
DifferentialExpression DESeq2
updated 2.2 years ago by ★ 5.0k • written 2.2 years ago by • 0
0
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3
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985
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The meaning of the analysis results when using a new metric in analysis
DESeq2
updated 2.2 years ago by 68k • written 2.2 years ago by ▴ 10
1
vote
1
reply
1.6k
views
Can I transform already normalized rna-seq data with Z-score?
Z-score RNASeqData Deseq DESeq2
updated 2.2 years ago by 68k • written 2.2 years ago by • 0
0
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1
reply
853
views
How to compared two groups out of twelve in DESeq2
DESeq2
updated 2.2 years ago by 68k • written 2.2 years ago by • 0
1
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7
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1.9k
views
Permutation test in DESeq2?
DESeq2
updated 2.2 years ago by 43k • written 2.2 years ago by • 0
3
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3
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1.1k
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EdgeR and DESeq2, variance estimation and parametric test
parametrictest edgeR DESeq2
2.2 years ago Nisha • 0
3
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5
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2.2k
views
Getting batch corrected counts after RUVSeq
BatchEffect RUVSeq RNASeq DESeq2
updated 2.2 years ago by ★ 5.0k • written 2.2 years ago by • 0
0
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1
reply
593
views
Run DESeq2 on chromosome and plasmids separately
DESeq2
updated 2.2 years ago by ★ 5.0k • written 2.2 years ago by ▴ 10
0
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1
reply
690
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Unable to create ddf object
DESeqDataSetFromMatrix dds DESeq2
updated 2.2 years ago by 68k • written 2.2 years ago by • 0
0
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2
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1.0k
views
RSubread DESeq2
RNASeqData DifferentialExpression DESeq2
2.2 years ago Beyza • 0
0
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3
replies
955
views
Dramatically different DESeq2 results in Mac and Linux computers
DESeq2
updated 2.2 years ago by 68k • written 2.2 years ago by ▴ 30
1
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2
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745
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Setting up a multi-factor experiement
DESeq2
2.2 years ago jon50250 • 0
0
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1
reply
853
views
DESeq design and contrast with multiple factors
RNASeq DESeq2
updated 2.2 years ago by 43k • written 2.3 years ago by • 0
1
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1
reply
1.2k
views
results after deseq2 not showing gene ids and gene names but they are present in dds object
DESeq2
updated 2.3 years ago by 68k • written 2.3 years ago by • 0
0
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3
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1.5k
views
DESeq2 not full rank with paired patient samples and one control cohort
DESeq2
updated 2.2 years ago by 68k • written 2.3 years ago by • 0
0
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3
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1.4k
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RNAseq (Deseq2 and Dexseq2) analysis on two time points with expected same effect
DEXSeq RNA-seq DESeq2
updated 2.3 years ago by ★ 1.9k • written 2.3 years ago by • 0
0
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1
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852
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Is it possible to combine count gene expression data coming from one sequencing technology (RNA seq) with intensity gene expression data coming from …
DESeq2 RNASeqData edgeR limma DifferentialExpression
updated 2.3 years ago by ★ 5.0k • written 2.3 years ago by • 0
0
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1
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1.2k
views
How to properly compare the group-specific samples using DEseq2
DESeq2
updated 2.3 years ago by ★ 1.4k • written 2.3 years ago by • 0
5
votes
13
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4.3k
views
Does countsFromAbundance="lengthScaledTPM" produce un-normalized counts?
tximport DESeq2
updated 2.2 years ago by 43k • written 2.3 years ago by • 0
0
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5
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1.6k
views
How to use contrast with multiple treatments?
RNASeqdataanalysis DESeq2
updated 2.3 years ago by ★ 1.4k • written 2.3 years ago by • 0
2
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2
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1.6k
views
DESeq2 results - Annotating and exporting results
DESeq2
updated 2.3 years ago by 68k • written 2.3 years ago by • 0
3
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7
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1.7k
views
DESeq2 alternative hypyothesis: testing for genes NOT significantly downregulated
DESeq2
2.3 years ago casco ▴ 10
0
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9
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1.7k
views
DESeq2: How to estimate effects of one factor controlling for other factors?
DESeq2
2.3 years ago mjd275 • 0
1
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8
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4.3k
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Significantly regulated genes produced by only a few affected samples
deseq2
written 7.7 years ago by ▴ 60
2
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12
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2.9k
views
P-value inflation?
DESeq2
updated 2.3 years ago by 68k • written 2.3 years ago by ▴ 10
1
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2
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1.4k
views
DESeq2 batch design
DESeq2
updated 2.3 years ago by ★ 1.4k • written 2.3 years ago by ▴ 10
0
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1
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1.1k
views
Getting NAs in both p-values (normal and adjusted) in DEseq2
DESeq2
updated 2.3 years ago by ★ 5.0k • written 2.3 years ago by • 0
8
votes
15
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3.3k
views
PCA percent variance DESeq2
PCA DESeq2
2.3 years ago IUH • 0
1
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6
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3.5k
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Time-series RNA-seq analysis using DESeq2
time-series DESeq2 RNASeq timecoursedata TimeCourse
updated 2.3 years ago by ★ 5.0k • written 2.3 years ago by • 0
0
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1
reply
932
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Comparing the effect of single drug and two-drug combination with control in RNA seq data
GeneExpressionWorkflow DESeq2
updated 2.3 years ago by 43k • written 2.3 years ago by • 0
0
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1
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638
views
DEG by deseq2 by Race
DESeq2
updated 2.3 years ago by ★ 4.0k • written 2.3 years ago by • 0
0
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1
reply
741
views
the confuse issue in DEseq2 among multi group
DESeq2
updated 2.3 years ago by 68k • written 2.3 years ago by • 0
3
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2
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2.8k
views
ERROR in EnrichKEGG(), 'species should be listed' in, download method do not change
KEGG DESeq2 biomaRt clusterProfiler org.Mm.eg.db
updated 2.3 years ago by ★ 4.1k • written 2.3 years ago by ▴ 10
5
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2
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1.8k
views
can't install DESeq2 ("unable to access index for repository")
biocmanager DESeq2
2.3 years ago Alessia ▴ 40
2
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5
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2.8k
views
removing the batch effect for vst counts and defining the batches in removeBatchEffect function
DESeq2 BatchEffect limma
updated 2.3 years ago by 53k • written 2.3 years ago by • 0
0
votes
1
reply
867
views
FALSE error when checking a pre made sample data
Rstudio scRNAseq DESeq2
updated 2.3 years ago by ★ 5.0k • written 2.3 years ago by • 0
4,840 results • Page 10 of 97
Recent ...
Replies
Answer: problem reading bam files into nucleR by James W. MacDonald 68k
The first step is to update to the current versions of R/Bioconductor and try again. It's possible that you have run into a bug that's alre…
Answer: Question about DESeq2 Design for Paired Treatment Study by ATpoint ★ 5.0k
It's a paired analysis so you don't need any patient-specific covariates such as age and sex. What you call batch effect might just be the …
Comment: problem reading bam files into nucleR by efoss ▴ 10
I thought I might be able to track down a problematic line in the bam file by repeatedly splitting the bam file in and then running the co…
Answer: two questions about limma by Gordon Smyth 53k
Answered here: https://support.bioconductor.org/p/16318/
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication? by Ahmed Salah • 0
Thank you very much! will take that into consideration
Votes
Upcoming Ensembl API and data access changes - new blog post available
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
Answer: Large logFC but somewhat high FDR
Comment: upstream git branches of bioc-release
Comment: upstream git branches of bioc-release
Awards • All
Popular Question to jared.andrews07 ▴ 30
Popular Question to James W. MacDonald 68k
Popular Question to shepherl 4.2k
Popular Question to Gordon Smyth 53k
Popular Question to k___ ▴ 30
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