Showing : DESEq2 • reset
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DESeq2 - nested samples (individuals) - time course - conditions
deseq2 nested de
updated 6.0 years ago by 43k • written 6.0 years ago by • 0
2
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3
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2.0k
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DESeq2: DE Analysis with very imbalanced samples per condition
deseq2 cancer
updated 22 months ago by • 0 • written 6.0 years ago by • 0
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1
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2.0k
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DESeq2 comparison of treatment within tissue type, ignoring other tissue type
deseq2 comparison design paired treatment
updated 6.0 years ago by ★ 1.4k • written 6.0 years ago by • 0
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7
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905
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DESeq2 resultsname problem
deseq2
updated 6.0 years ago by 43k • written 6.0 years ago by • 0
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1
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1.1k
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DESeq2 analysis. Understanding results() and the design formula.
deseq2
updated 6.0 years ago by ★ 1.4k • written 6.0 years ago by • 0
2
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3
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1.9k
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DESeq2 2x2 factorial design: find genes unique to factor A?
deseq2 deseq differential expression contrasts
updated 6.0 years ago by 43k • written 6.0 years ago by ▴ 180
1
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3
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822
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Is DESeq2 normalisation method appropriate for datasets with multiple cell types?
deseq2 normalization
updated 6.0 years ago by 43k • written 6.0 years ago by ▴ 10
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1
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863
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Unable to run DESeq command in DESeq2 without transforming data
deseq2
updated 6.0 years ago by 43k • written 6.0 years ago by • 0
0
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1
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558
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DESeq2 and the relevance of p-value in a time course analysis
deseq2
updated 6.0 years ago by 43k • written 6.0 years ago by • 0
1
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4
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3.1k
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Removal of batch effects from RNA-seq data for WGCNA
limma deseq2 wgcna RUVseq
6.0 years ago Arindam ▴ 80
0
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1
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669
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Question regarding p-values in deseq2
deseq2 p-values normalization
updated 6.0 years ago by 43k • written 6.0 years ago by • 0
1
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2
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3.4k
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DESeq2 - VST eliminates zero values
deseq2
updated 6.0 years ago by 43k • written 6.0 years ago by • 0
5
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3
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1.0k
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batch correction in DESeq2 > matrix not full rank > mitigate
DESeq2 batch correction
updated 6.0 years ago by 68k • written 6.0 years ago by ▴ 10
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1
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643
views
library normalization for DESeq2 using mapping proportions
deseq2 normalization
updated 6.0 years ago by 43k • written 6.0 years ago by ▴ 90
3
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5
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2.9k
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Question regarding "low counts" in DESeq2
deseq2
updated 6.0 years ago by 43k • written 6.0 years ago by • 0
1
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2
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931
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Label points on DESeq2 MA plot with interval list
deseq2 maplot annotation
updated 6.0 years ago by 43k • written 6.0 years ago by ▴ 60
2
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6
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5.6k
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removing genes before RNA-seq normalization
edger deseq2 normalization removing genes
updated 3.6 years ago by 53k • written 6.1 years ago by ▴ 90
0
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1
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563
views
A question about the results of DESeq2
deseq2 annotation
updated 6.0 years ago by ★ 4.0k • written 6.0 years ago by • 0
0
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1
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1.2k
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How to handle batch effect and interaction with experimental variables
deseq2 statistics differential expression
6.1 years ago A • 0
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2
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1.1k
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same results changing contrast function
deseq2 contrast DEG
updated 6.1 years ago by 43k • written 6.1 years ago by • 0
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1
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658
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Choosing and fixing the denominator in DESeq2 analysis
deseq2
updated 6.1 years ago by 43k • written 6.1 years ago by • 0
2
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1
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986
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Suitability of Deseq2 for analysis of different environmental metagenomes (DNA)
deseq2
updated 6.1 years ago by 43k • written 6.1 years ago by ▴ 10
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4
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1.1k
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DESeq2 likelihood ratio test (LRT) design
deseq2
6.1 years ago ijvechetti ▴ 10
0
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1
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921
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Is DESeq2 performs the same when I am loading library DESeq2?
DESeq2
6.8 years ago • updated 6.1 years ago AZ ▴ 30
1
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3
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1.6k
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RNAseq PCA resembles subject-specific effect in a paired study design
salmon DESeq2
updated 6.1 years ago by ★ 4.0k • written 6.1 years ago by ▴ 10
1
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1
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1.3k
views
DESeq2 Analysis of RNA-Edited Reads and Circular RNA
deseq2 circRNA rna-editing
updated 6.1 years ago by 43k • written 6.1 years ago by • 0
0
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8
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1.1k
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Variance assumptions in DESeq2 with blocks of linkage disequilibrium/chromosomal inversions
deseq2 normalization
updated 6.1 years ago by 43k • written 6.1 years ago by • 0
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3
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1.3k
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Can I use translation efficiency counts (Ribosome profiling TPM/RNASeq TPM) as an input for DESq2 in order to perform Differential Translation analys…
deseq2 differential translation ribosome profiling
updated 6.1 years ago by 43k • written 6.1 years ago by • 0
1
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2
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1.0k
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Why does dispersion estimation in DESeq2 depend on the design formula?
deseq2
updated 6.1 years ago by 43k • written 6.1 years ago by ▴ 10
2
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5
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1.4k
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How Does DESeq2 estimate dispersions?
DESeq2 Ribo-Seq
updated 6.1 years ago by 68k • written 6.1 years ago by • 0
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1
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1.1k
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DESeq2 outlier replacement with respect to continuous variable
deseq2
updated 6.1 years ago by 43k • written 6.1 years ago by • 0
2
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3
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1.1k
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DESeq2 doesn't return the most drastically DEG
deseq2 tcga
6.1 years ago ndjayne • 0
0
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8
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3.9k
views
DESeq2 PC1 variance on the PCA plot does not match proportion of variance
deseq2
updated 6.1 years ago by 43k • written 6.1 years ago by ▴ 190
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2
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1.0k
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DESeq2 design formula and lfcShrink() questions
deseq2
updated 6.1 years ago by 43k • written 6.1 years ago by ▴ 10
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2
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651
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Multi-group design when performing DE analysis
deseq2
updated 6.1 years ago by ★ 4.0k • written 6.1 years ago by • 0
1
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5
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1.8k
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edgeR or DESeq2 between duplicated chromosomes in the same individual
deseq2 edgeR normalization DGE
updated 6.1 years ago by 53k • written 6.1 years ago by ▴ 10
3
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2
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2.3k
views
batch effect correction for TCGA RNAseq harmonized data
deseq2 limma
updated 6.1 years ago by 43k • written 6.1 years ago by ▴ 20
0
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2
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949
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DESeq2 lfcShrink apeglm
deseq2
updated 6.1 years ago by 43k • written 6.1 years ago by • 0
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3
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1.2k
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Once again: Analyze Paired Samples from DESeq2 Vignette design formula and how to interprete
deseq2
updated 6.1 years ago by 43k • written 6.1 years ago by ▴ 30
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1
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4.2k
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DESeq2: What is the unit of DESeq2 normalized read count (VST)? Is it tag per million?
deseq2 vst rlog
updated 6.1 years ago by 43k • written 6.1 years ago by • 0
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2
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1.4k
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Correcting a nested batch effect
deseq2
updated 6.1 years ago by 43k • written 6.1 years ago by • 0
2
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4
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908
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Very variable samples vs similar samples in the same dataset
edger deseq2
updated 6.1 years ago by 43k • written 6.1 years ago by • 0
0
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3
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1.6k
views
Problem with DESeq2 object
deseq2 Biocodunctor
updated 6.1 years ago by 43k • written 6.1 years ago by • 0
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1
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1.2k
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Exclude interaction terms from the design
deseq2 statistics modelling
updated 6.1 years ago by 43k • written 6.1 years ago by • 0
2
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2
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3.8k
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DESeq2: design = ~1 For Normalisation Only.
deseq2 limma normalization tcga rnaseq
updated 6.1 years ago by 43k • written 6.1 years ago by • 0
0
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2
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690
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Biased results of DESeq2 LRT (Group name order)
deseq2
updated 6.1 years ago by 43k • written 6.1 years ago by • 0
0
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3
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4.5k
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What is lfcSE and how is it calculated?
deseq2 standarderror
6.1 years ago lizzid • 0
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3
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1.0k
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What are size factors used for in baseMean calculation
deseq2
updated 6.1 years ago by 43k • written 6.1 years ago by • 0
0
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2
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1.4k
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DEseq2 loading library problem
deseq2
updated 6.1 years ago by 25k • written 6.1 years ago by • 0
0
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1
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720
views
DESeq2 installation issue
deseq2
updated 6.1 years ago by 25k • written 6.1 years ago by • 0
4,840 results • Page 45 of 97
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Replies
Comment: 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
Comment: Large logFC but somewhat high FDR by JKim • 0
Thank you very much for taking the time to answer the question. I really appreciate your insights and comments.
Votes
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
Comment: upstream git branches of bioc-release
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