Showing : DESEq2 • reset
6
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Centering and scaling numeric variables
deseq2
updated 5.7 years ago by ▴ 40 • written 5.7 years ago by ▴ 30
0
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4
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735
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How to know what genes are differentially expression in DESeq2 simulation?
deseq2
updated 5.7 years ago by ★ 4.0k • written 5.7 years ago by • 0
0
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1
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374
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Choosing DESeq2 design
deseq2
updated 5.7 years ago by 43k • written 5.7 years ago by • 0
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3
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1.2k
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DE analysis outlier removal
deseq2 outlier normalization removal
updated 5.7 years ago by 43k • written 5.7 years ago by • 0
0
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1
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863
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DESeq dispersion parameter
deseq2
updated 5.7 years ago by 43k • written 5.7 years ago by • 0
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2
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1.0k
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phyloseq_to_deseq2 design strategy for multiple factors analysis (2 or more)
deseq2
updated 5.7 years ago by 43k • written 5.7 years ago by • 0
5
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2
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1.7k
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DESeq2 pairwise comparisons w/ 3 factors
deseq2
updated 5.7 years ago by 43k • written 5.7 years ago by ▴ 10
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6
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1.7k
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Remove batch effect for DESeq2
deseq2
updated 5.7 years ago by 68k • written 5.7 years ago by • 0
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3
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2.1k
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DESeq2 - cannot find function?
deseq2 r software error
updated 5.7 years ago by 43k • written 5.7 years ago by • 0
4
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3
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1.2k
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RNA-Seq analysis with DESeq2: showing two conditions do *not* significantly differ
deseq2 RNA-Seq uniform distribution data visualization
updated 5.7 years ago by ★ 13k • written 5.7 years ago by ▴ 20
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1
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358
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DESeq2 : Model clarification
deseq2
updated 5.7 years ago by 43k • written 5.7 years ago by ▴ 20
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8
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3.4k
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DESeq LRT reduced model
deseq2 LRT
updated 5.7 years ago by 43k • written 5.7 years ago by • 0
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5
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1.2k
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Negative Binomial model for microbiome data
deseq2
updated 5.7 years ago by 43k • written 5.7 years ago by • 0
1
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1
reply
7.1k
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How to import featureCounts data into DESeq2
DESEq2
updated 5.7 years ago by 43k • written 5.7 years ago by • 0
0
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1
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1.4k
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Adjusting for unwanted variation in DESeq2
DESeq2 deseq2 sva rna-seq differential expression anlaysis
updated 5.7 years ago by 68k • written 5.7 years ago by • 0
1
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1
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1.1k
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multifactor desing with interaction LRT or Wald test?
deseq2 LRT wald
updated 5.7 years ago by ★ 4.0k • written 5.7 years ago by ▴ 10
0
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1
reply
790
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Meaning of log2 fold change in 2 x 4 interaction
deseq2
updated 5.7 years ago by 43k • written 5.7 years ago by ▴ 10
1
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3
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2.2k
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In DESeq2, how do you interpret results based on the order of variables in the "contrast" argument?
deseq2
updated 5.7 years ago by ★ 4.0k • written 5.7 years ago by • 0
1
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1
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564
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mate pairs read counts as input for DESeq2
deseq2
updated 5.7 years ago by 68k • written 5.7 years ago by ▴ 10
1
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2
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1.1k
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Data not getting normalised after DESeq2
deseq2 normalization
updated 5.7 years ago by 43k • written 5.7 years ago by ▴ 40
3
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6
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961
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MA plot shows inflation of downregulated genes.
deseq2
updated 5.7 years ago by 43k • written 5.7 years ago by ▴ 10
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1
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3.3k
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Where in the procedure do I remove low-expressed genes?
deseq2 edger
updated 5.7 years ago by 43k • written 5.7 years ago by • 0
0
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3
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1.3k
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DESeq2 accounting for two confounders with interaction in the design matrix
deseq2 design matrix multi-confounders linear models rna-seq
updated 5.7 years ago by 43k • written 5.7 years ago by • 0
1
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3
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1.4k
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DESeq2 - controlling for other variables
deseq2 DEG covariate study design variables
updated 5.7 years ago by 43k • written 5.7 years ago by • 0
1
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1
reply
484
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DESeq2: Identify similarly expressed genes
deseq2
updated 5.7 years ago by 43k • written 5.7 years ago by • 0
0
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8
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1.4k
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DESeq2 notice about GLM convergence
deseq2 RNASeq
updated 5.7 years ago by 43k • written 5.7 years ago by • 0
3
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3
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2.0k
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Repeated error loading DESqe2 - package xxx not found
deseq2 package software error
updated 5.7 years ago by 25k • written 5.8 years ago by • 0
0
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6
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2.1k
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Bizarre Dispersion Plots
deseq2 RNA RNASeq
updated 5.8 years ago by 43k • written 5.8 years ago by • 0
2
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2
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1.3k
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RNA-seq analysis with DESeq2
deseq2
updated 5.8 years ago by ▴ 280 • written 5.8 years ago by ▴ 50
2
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8
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1.5k
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DESEQ2 design with unequal matching and replicates?
deseq2 RNASeq
updated 5.8 years ago by 43k • written 5.8 years ago by • 0
2
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3
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730
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The basis for the full rank design matrix requirement in DESeq2
deseq2
updated 5.8 years ago by 43k • written 5.8 years ago by ▴ 90
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2
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735
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DESeq2 error on function results
deseq2
updated 5.8 years ago by 43k • written 5.8 years ago by • 0
0
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1
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1.4k
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What does an asymmetrical MA plot indicate and how do I know if it means I've made an error?
deseq2 plotMA rnaseq community analysis asymmetry
updated 5.8 years ago by 43k • written 5.8 years ago by • 0
2
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3
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724
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Order of levels within factors affects DESeq2 results when interaction is included
deseq2
updated 5.8 years ago by 43k • written 5.8 years ago by • 0
1
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5
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732
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subtle differences in results based on how Design Table is coded
deseq2
updated 5.8 years ago by 43k • written 5.8 years ago by • 0
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0
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922
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News: RNAseq data analysis with R and Bioconductor
limma deseq2 go edger News
5.8 years ago info ▴ 10
0
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3
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1.2k
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how to interpret results from 3way design in DESeq2
deseq2
updated 5.8 years ago by 43k • written 5.8 years ago by • 0
0
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3
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1.6k
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Highly variable gene analysis including RUVs batch correction
deseq2 RUV batch highly variable genes
updated 5.8 years ago by • 0 • written 5.8 years ago by • 0
4
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5
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1.7k
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Difference in dimensionality reduction plots based on DESeq2 R package and core functions for RNA-Seq data
deseq2 vst pca cpm
5.8 years ago svlachavas ▴ 840
2
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8
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3.4k
views
DESeq2 : log2FC discrepencies between results and lfcShrink
deseq2 shrinkage
updated 3.0 years ago by 43k • written 5.8 years ago by ▴ 20
2
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4
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1.6k
views
DESeq2 - problem with inferring correct results.
deseq2 rnaseq sva fdrtool ihw
updated 5.8 years ago by 43k • written 5.8 years ago by • 0
0
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7
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1.7k
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tximeta doesn't work downloading the ref genome
deseq2 tximeta tximport rnaseq
5.8 years ago rafaelsolersanblas ▴ 50
1
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2
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1.8k
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For loop for DESeq2
loop deseq2 rnaseq
updated 3.4 years ago by • 0 • written 5.8 years ago by ▴ 10
0
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1
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599
views
DESeq2: basemean count
deseq2
updated 5.8 years ago by 43k • written 5.8 years ago by ▴ 120
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1
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509
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DESeq2: multiple factors, comparison of a main factor between samples with inconsistent magnitudes of gene expression changes
deseq2
updated 5.8 years ago by 43k • written 5.8 years ago by ▴ 10
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1
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1.1k
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DESeq2 with uneven group size
deseq2
updated 5.8 years ago by 43k • written 5.8 years ago by • 0
0
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1
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2.5k
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RLE plot of DESeq2 normalisation / extract matrix of normalised counts from DESeqDataSet
deseq2 RLE
updated 5.8 years ago by 43k • written 5.8 years ago by • 0
1
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3
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1.1k
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DESeq2 : Estimating dispersions takes forever to finish
deseq2
5.8 years ago Nicolas Rosewick ▴ 20
3
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5
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1.8k
views
Emirical Bayesian shrinkage for dispertion/LFC estimation
rnaseq deseq2
updated 5.8 years ago by 43k • written 5.8 years ago by ▴ 10
1
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2
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582
views
I have four groups in my RNAseq experiment and want to compare them all to each other (not them all to a control). How do I do this is deseq2?
deseq2
updated 5.8 years ago by ★ 1.4k • written 5.8 years ago by • 0
4,840 results • Page 42 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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