Showing : DESeq • reset
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DESeq2 "Not full rank" and "less than full rank" error
DESeq2 deseq
updated 9 weeks ago by ★ 4.1k • written 9 weeks ago by • 0
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614
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evaluate the variable importance on genes
DESeq2 deseq
11 months ago Meme • 0
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2
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563
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Running DESeq on normalized data
deseq DESeq2
updated 13 months ago by ★ 4.6k • written 13 months ago by • 0
2
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2
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828
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Predicting missing values splines DESeq2
deseq DESeq2
14 months ago georgii.vdovin • 0
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601
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Controling for Covariates With a Continuous Predictor Variable
Deseq DESeq2
updated 14 months ago by 43k • written 14 months ago by • 0
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1
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1.2k
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Can I transform already normalized rna-seq data with Z-score?
Z-score RNASeqData Deseq DESeq2
updated 16 months ago by 67k • written 16 months ago by • 0
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3
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2.7k
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Difference between DESeqDataSetFromMatrix() function and DESeq() function
DESeq DESeq2
updated 17 months ago by ★ 4.6k • written 17 months ago by ▴ 10
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4
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968
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lfc direction of effect flipped for ashr, apeGLM, but accurate to biological data for non-shrunken
DESeq2 apeglm DESeq ApeGLM Ashr
updated 18 months ago by 43k • written 18 months ago by ▴ 20
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952
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summarizeToGene in tximeta causing vastly different results
DESeq2 deseq txime tximeta
updated 21 months ago by 43k • written 21 months ago by • 0
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4
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2.0k
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Volcano plot becomes flipped when I add a third condition
DESeq2 volcanoplot deseq HELP contrast
updated 23 months ago by ▴ 780 • written 23 months ago by • 0
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761
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What is the difference between these two arguments for log fold change shrinkage?
DESeq
updated 24 months ago by 43k • written 24 months ago by ▴ 10
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990
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Is it possible to convert transcript-level to gene-level dataset to use it in DESeq2 ?
DESeq2 Transcriptomics tximport deseq txi
updated 2.0 years ago by ★ 1.5k • written 2.0 years ago by ▴ 10
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1.5k
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suggestions/comments on DESeq transcript wise analysis
convert DESeq convert DESeq
written 13.0 years ago by ▴ 190
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1
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694
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How to design multifactor DESEQ2 formula?
DESEQ DESEQ2
updated 2.4 years ago by ★ 4.6k • written 2.4 years ago by • 0
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2
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1.2k
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DESeq2 is renaming gene names and lack of downregulated genes
DESeq DESeq2
2.5 years ago manwar • 0
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1
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1.0k
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Gene wise dispersion estimate Process - From the prior to the posterior
GLM prior DESeq LFC
updated 2.6 years ago by 43k • written 2.6 years ago by • 0
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5
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1.5k
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Error in DEseq
DEseq RNASeqData
updated 2.6 years ago by ★ 4.6k • written 2.6 years ago by • 0
2
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1
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1.9k
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Difference between raw counts and featureCounts for DESeq2
deseq featurecounts counts DESeq2
updated 2.7 years ago by ★ 1.4k • written 2.7 years ago by ▴ 10
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5
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1.8k
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Potential outlier/high variance
deseq DESeq2
updated 2.7 years ago by 43k • written 2.8 years ago by • 0
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2
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1.1k
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Deseq2 with imbalanced design
Deseq
2.9 years ago • updated 2.8 years ago Alex • 0
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4
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2.0k
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Test if a gene is NOT differentially expressed in DESeq2?
DESeq2 deseq
updated 3.0 years ago by 43k • written 3.0 years ago by • 0
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2
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1.4k
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DESeqDataSet design issue
DESeq DESeq2
3.1 years ago matthew.valentine • 0
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1
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1.9k
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DESeq2 rows did not converge in beta, how to solve
DESeq DESeq2
updated 3.2 years ago by 43k • written 3.2 years ago by • 0
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6
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2.1k
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Interpretation of DESeq2 results with 3 factorial design with interaction terms.
r DESeq DESeq2
3.3 years ago s-rhussien • 0
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2
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2.6k
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Correct way to make multiple comparisons on DESeq2?
DESeq DESeq2 R
3.4 years ago jbnrodriguez ▴ 10
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2
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1.2k
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DESeq2 log2Foldchanges opposite sign for almost the same groups of comparison
RNASeq DESeq
3.4 years ago krawczyk.margarita • 0
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2
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1.9k
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same padj for all the genes after DEseq analysis
etLRT WALD edgeR DESEq
updated 3.4 years ago by 43k • written 3.4 years ago by • 0
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1
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1.4k
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Filtering DESeq2 results for | LFC | > 1 genes
RNAseq LFC DEseq
3.7 years ago ayy2110 • 0
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2
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1.2k
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metage problem with DESeq
DESeq metagene2 metagene
updated 3.8 years ago by ▴ 10 • written 3.9 years ago by ▴ 10
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3
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3.2k
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Understanding MA plot distortion
DESeq2 MAplot deseq
updated 3.9 years ago by 43k • written 3.9 years ago by • 0
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5
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2.2k
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ZINB-WaVE-DESeq2 with Bulk Data: Choice of Epsilon value, K and gene number
DESeq2 ZINB zinbwave deseq
updated 4.0 years ago by 43k • written 4.0 years ago by • 0
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12
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5.1k
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Deseq2: How to adjust for baseline read counts when testing for groups differences at post-treatment
deseq2 deseq
updated 4.2 years ago by 43k • written 9.7 years ago by • 0
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2
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1.2k
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DESeq Error (nbinomTest ())
Deseq nbinomTest
4.6 years ago canfield ▴ 10
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7
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2.4k
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DESeq error: Error in validityMethod(object) : nrow(design) == ncol(object) is not TRUE
deseq2 DESeq nrow == ncol is not TRUE
updated 4.7 years ago by ★ 4.0k • written 4.7 years ago by • 0
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5
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6.6k
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ERROR configuration failed for package RCurl during installation of DESeq
ERROR: configuration failed for package ‘RCurl’ DESeq
written 4.8 years ago by ▴ 10
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2
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1.1k
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Mocking data for understanding interactions in DESeq2
deseq2 deseq
updated 4.8 years ago by ★ 3.8k • written 4.8 years ago by • 0
3
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5
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2.6k
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How to analyze pre-processed RNA-Seq data from GEO based on the deseq R package for filtering and DE analysis
deseq rna-seq filtering DE deseq2
updated 4.8 years ago by 43k • written 4.8 years ago by ▴ 840
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9
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1.6k
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Wrong results of DESeq compared to DESeq2 for some test cases?
deseq2 DESeq
updated 4.8 years ago by ★ 3.8k • written 4.8 years ago by • 0
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7
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1.5k
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how to analyze and find differentially expressed genes based on miRNA gene raw read counts?
deseq2 deseq
5.0 years ago MANYA_BIOINFO • 0
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1.5k
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DESeq2 counts function not working
deseq2 Deseq RNAseq
updated 5.1 years ago by 43k • written 5.1 years ago by ▴ 10
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3
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1.6k
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DESeq2 2x2 factorial design: find genes unique to factor A?
deseq2 deseq differential expression contrasts
updated 5.2 years ago by 43k • written 5.2 years ago by ▴ 180
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4
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5.4k
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TMM Normalization: DESeqDataSet: some values in assay are negative
deseq2 deseq normalization
updated 5.5 years ago by ▴ 40 • written 5.5 years ago by • 0
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2
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1.1k
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Filtering extraneous samples affects DESeq results. What is going on?
deseq deseq2
updated 5.5 years ago by 43k • written 5.5 years ago by • 0
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0
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1.2k
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Including sva results in SeqGSEA with data with batch effect
limma deseq2 seqgsea sva deseq
5.5 years ago kentfung ▴ 20
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9
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2.4k
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NOOB question: How to use contrasts for subgroup analysis in DESeq2?
deseq deseq2 contrast subgroup
5.9 years ago ariel ▴ 20
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12
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2.0k
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Why did I get NA p-values in DESeq with continuous variable?
deseq2 p-value continuous deseq
5.9 years ago ariel ▴ 20
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3
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2.2k
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DESeq2 count outlier replacement from Cook's threshold
deseq2 deseq rnaseq outliers count outliers
updated 6.1 years ago by 43k • written 6.1 years ago by ▴ 10
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1
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1.2k
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Question about multi-factor Deseq analysis
DESeq deseq2 microbiome gut microbiome
updated 6.2 years ago by 43k • written 6.2 years ago by • 0
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3
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1.4k
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Strange lfcShrink plot when running DESeq2 workflow
DESeq2 rnaseq rna-seq deseq2 deseq
6.3 years ago Ben ▴ 50
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7
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4.2k
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DESeq2 install problem
deseq
updated 6.3 years ago by 43k • written 6.3 years ago by • 0
50 results • Page 1 of 1
Recent ...
Replies
Comment: Are unequal sample sizes in differential gene expression (DGE) analysis a proble by Amora • 0
Both edgeR and DESeq2 can handle unequal group sizes if you ensure proper quality control and variance estimation. [sprunki retake][1] …
Comment: Announcing GBCC 2025: The first-ever joint conference between Bioconductor and G by Amora • 0
You did a great job giving an overview.....[slope][1] better than the bioconductor group! [1]: https://slopeio.org
Comment: contrast matrix design for a continuous variable by dtzhu337 • 0
Hi Gordon, Thank you very much for your answer. Actually the variable X is the age, which I am also interested in. Somehow, age and V1 are…
Answer: SingleCellExperiment convenience function for metadata+expression? by Peter Hickey ▴ 750
Hi Sarah, `scuttle::makePerCellDF()` / `scuttle::makePerFeatureDF()` and `scater::ggcells()` / `scater::ggfeatures()`, which build upon th…
Comment: How to sort negative log2FC or FC in RNAseq for GSEA? by QN ▴ 10
Thank you ATpoint for your response! In the result of GSEA, like you indicated, there will be gene sets that have positive NES and gene se…
Votes
Answer: SingleCellExperiment convenience function for metadata+expression?
How to correct for tumor purity using DESeq2 to analyze TCGA tumor sample expression.
Answer: EdgeR Biological CVs
Answer: Error in download.file for TCGAutils::symbolsToRanges
Answer: Error in download.file for TCGAutils::symbolsToRanges
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Popular Question to Peter Hickey ▴ 750
Popular Question to Gordon Smyth 52k
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