Showing : DESeq • reset
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DESeq2 "Not full rank" and "less than full rank" error
DESeq2 deseq
updated 3 months ago by ★ 4.1k • written 3 months ago by • 0
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648
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evaluate the variable importance on genes
DESeq2 deseq
12 months ago Meme • 0
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2
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600
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Running DESeq on normalized data
deseq DESeq2
updated 14 months ago by ★ 4.7k • written 14 months ago by • 0
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2
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882
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Predicting missing values splines DESeq2
deseq DESeq2
15 months ago georgii.vdovin • 0
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638
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Controling for Covariates With a Continuous Predictor Variable
Deseq DESeq2
updated 16 months ago by 43k • written 16 months ago by • 0
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1.3k
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Can I transform already normalized rna-seq data with Z-score?
Z-score RNASeqData Deseq DESeq2
updated 17 months ago by 68k • written 17 months ago by • 0
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3
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3.1k
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Difference between DESeqDataSetFromMatrix() function and DESeq() function
DESeq DESeq2
updated 19 months ago by ★ 4.7k • written 19 months ago by ▴ 10
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4
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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 19 months ago by 43k • written 19 months ago by ▴ 20
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998
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summarizeToGene in tximeta causing vastly different results
DESeq2 deseq txime tximeta
updated 22 months ago by 43k • written 22 months ago by • 0
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4
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Volcano plot becomes flipped when I add a third condition
DESeq2 volcanoplot deseq HELP contrast
updated 2.0 years ago by ▴ 780 • written 2.0 years ago by • 0
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790
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What is the difference between these two arguments for log fold change shrinkage?
DESeq
updated 2.1 years ago by 43k • written 2.1 years ago by ▴ 10
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1.0k
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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 2.1 years ago by ★ 1.6k • written 2.1 years ago by ▴ 10
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suggestions/comments on DESeq transcript wise analysis
convert DESeq convert DESeq
written 13.1 years ago by ▴ 190
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1
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727
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How to design multifactor DESEQ2 formula?
DESEQ DESEQ2
updated 2.5 years ago by ★ 4.7k • written 2.5 years ago by • 0
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1.2k
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DESeq2 is renaming gene names and lack of downregulated genes
DESeq DESeq2
2.6 years ago manwar • 0
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1
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1.1k
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Gene wise dispersion estimate Process - From the prior to the posterior
GLM prior DESeq LFC
updated 2.7 years ago by 43k • written 2.7 years ago by • 0
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5
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1.6k
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Error in DEseq
DEseq RNASeqData
updated 2.7 years ago by ★ 4.7k • written 2.7 years ago by • 0
2
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1
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2.0k
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Difference between raw counts and featureCounts for DESeq2
deseq featurecounts counts DESeq2
updated 2.8 years ago by ★ 1.4k • written 2.8 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 2.8 years ago by 43k • written 2.9 years ago by • 0
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2
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1.2k
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Deseq2 with imbalanced design
Deseq
3.0 years ago Alex • 0
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4
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2.1k
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Test if a gene is NOT differentially expressed in DESeq2?
DESeq2 deseq
updated 3.1 years ago by 43k • written 3.1 years ago by • 0
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2
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1.5k
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DESeqDataSet design issue
DESeq DESeq2
3.2 years ago matthew.valentine • 0
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2.0k
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DESeq2 rows did not converge in beta, how to solve
DESeq DESeq2
updated 3.3 years ago by 43k • written 3.3 years ago by • 0
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6
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2.2k
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Interpretation of DESeq2 results with 3 factorial design with interaction terms.
r DESeq DESeq2
3.4 years ago s-rhussien • 0
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2
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2.7k
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Correct way to make multiple comparisons on DESeq2?
DESeq DESeq2 R
3.5 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
3.5 years ago krawczyk.margarita • 0
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2.0k
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same padj for all the genes after DEseq analysis
etLRT WALD edgeR DESEq
updated 3.5 years ago by 43k • written 3.6 years ago by • 0
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1.4k
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Filtering DESeq2 results for | LFC | > 1 genes
RNAseq LFC DEseq
3.8 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 4.0 years ago by ▴ 10 • written 4.0 years ago by ▴ 10
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3
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3.4k
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Understanding MA plot distortion
DESeq2 MAplot deseq
updated 4.0 years ago by 43k • written 4.0 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 4.1 years ago by 43k • written 4.1 years ago by • 0
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12
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5.2k
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Deseq2: How to adjust for baseline read counts when testing for groups differences at post-treatment
deseq2 deseq
updated 4.3 years ago by 43k • written 9.8 years ago by • 0
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1.2k
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DESeq Error (nbinomTest ())
Deseq nbinomTest
4.7 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 4.8 years ago by ★ 4.0k • written 4.8 years ago by • 0
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5
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6.8k
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ERROR configuration failed for package RCurl during installation of DESeq
ERROR: configuration failed for package ‘RCurl’ DESeq
written 4.9 years ago by ▴ 10
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2
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1.2k
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Mocking data for understanding interactions in DESeq2
deseq2 deseq
updated 4.9 years ago by ★ 3.8k • written 4.9 years ago by • 0
3
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5
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2.7k
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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 4.9 years ago by 43k • written 4.9 years ago by ▴ 840
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9
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1.7k
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Wrong results of DESeq compared to DESeq2 for some test cases?
deseq2 DESeq
updated 5.0 years ago by ★ 3.8k • written 5.0 years ago by • 0
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7
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1.6k
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how to analyze and find differentially expressed genes based on miRNA gene raw read counts?
deseq2 deseq
5.1 years ago MANYA_BIOINFO • 0
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1.6k
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DESeq2 counts function not working
deseq2 Deseq RNAseq
updated 5.2 years ago by 43k • written 5.2 years ago by ▴ 10
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3
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1.7k
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DESeq2 2x2 factorial design: find genes unique to factor A?
deseq2 deseq differential expression contrasts
updated 5.3 years ago by 43k • written 5.3 years ago by ▴ 180
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4
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5.6k
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TMM Normalization: DESeqDataSet: some values in assay are negative
deseq2 deseq normalization
updated 5.6 years ago by ▴ 40 • written 5.6 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 5.6 years ago by 43k • written 5.6 years ago by • 0
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Including sva results in SeqGSEA with data with batch effect
limma deseq2 seqgsea sva deseq
5.7 years ago kentfung ▴ 20
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9
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2.5k
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NOOB question: How to use contrasts for subgroup analysis in DESeq2?
deseq deseq2 contrast subgroup
6.0 years ago ariel ▴ 20
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12
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2.1k
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Why did I get NA p-values in DESeq with continuous variable?
deseq2 p-value continuous deseq
6.0 years ago ariel ▴ 20
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3
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2.3k
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DESeq2 count outlier replacement from Cook's threshold
deseq2 deseq rnaseq outliers count outliers
updated 6.2 years ago by 43k • written 6.2 years ago by ▴ 10
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1.2k
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Question about multi-factor Deseq analysis
DESeq deseq2 microbiome gut microbiome
updated 6.3 years ago by 43k • written 6.3 years ago by • 0
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3
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1.5k
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Strange lfcShrink plot when running DESeq2 workflow
DESeq2 rnaseq rna-seq deseq2 deseq
6.4 years ago Ben ▴ 50
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7
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4.2k
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DESeq2 install problem
deseq
updated 6.4 years ago by 43k • written 6.4 years ago by • 0
50 results • Page 1 of 1
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Replies
Comment: how many significant figures are there in DESeq2 output by ATpoint ★ 4.7k
If you want consistency then use a fixed software environment like Docker, wirh fixed code and thresholds that make sense. Rounding to near…
Comment: Compare TCGA-PAAD with GTEx gene expression by Jane • 0
why aren't there any answers?
Comment: Too many significant genes when integrating gtex and tcga by Jane • 0
I encountered the same issue: too many DEGs after limma analysis. It is sad that until today we can still see the paper published where GTE…
Comment: how many significant figures are there in DESeq2 output by Matthew McCormack ▴ 180
Thank you for your reply. It is good to know that cutoff of 0.05 means less than 0.05. My concerns are about consistency and reproducibili…
Comment: DiffBind edgeR normalization --- why are the normalization factors all equal to by ATpoint ★ 4.7k
No, normalization factors from edgeR rather than size factors from DESeq2 are not proportional, it's a different concept and implementation…
Votes
A: Unbalanced experiment with multiple samples from each patient.
Unbalanced experiment with multiple samples from each patient.
Answer: Vertical line at A=0, nothing else, on MA plot
Answer: GSVA Error Code "Calling gsva(expr=., gset.idx.list=., method=., ...) is defunct
Answer: Group-specific condition effects with individuals nested: matrix is not full ra
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