Showing : deseq • reset
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evaluate the variable importance on genes
DESeq2 deseq
12 weeks ago Meme • 0
0
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2
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350
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Running DESeq on normalized data
deseq DESeq2
updated 5 months ago by ★ 4.1k • written 5 months ago by • 0
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2
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541
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Predicting missing values splines DESeq2
deseq DESeq2
6 months ago • updated 5 months ago georgii.vdovin • 0
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1
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395
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Controling for Covariates With a Continuous Predictor Variable
Deseq DESeq2
updated 6 months ago by 42k • written 6 months ago by • 0
0
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1
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682
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Can I transform already normalized rna-seq data with Z-score?
Z-score RNASeqData Deseq DESeq2
updated 8 months ago by 65k • written 8 months ago by • 0
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3
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977
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Difference between DESeqDataSetFromMatrix() function and DESeq() function
DESeq DESeq2
updated 9 months ago by ★ 4.1k • written 9 months ago by ▴ 10
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4
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673
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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 10 months ago by 42k • written 10 months ago by ▴ 20
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2
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633
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summarizeToGene in tximeta causing vastly different results
DESeq2 deseq txime tximeta
updated 13 months ago by 42k • written 13 months ago by • 0
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4
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1.3k
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Volcano plot becomes flipped when I add a third condition
DESeq2 volcanoplot deseq HELP contrast
updated 15 months ago by ▴ 780 • written 15 months ago by • 0
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1
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576
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What is the difference between these two arguments for log fold change shrinkage?
DESeq
updated 15 months ago by 42k • written 15 months ago by ▴ 10
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1
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747
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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 16 months ago by ★ 1.5k • written 16 months ago by ▴ 10
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2
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1.3k
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suggestions/comments on DESeq transcript wise analysis
convert DESeq convert DESeq
written 12.3 years ago by ▴ 190
1
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1
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533
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How to design multifactor DESEQ2 formula?
DESEQ DESEQ2
updated 20 months ago by ★ 4.1k • written 20 months ago by • 0
3
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2
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943
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DESeq2 is renaming gene names and lack of downregulated genes
DESeq DESeq2
22 months ago manwar • 0
1
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1
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790
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Gene wise dispersion estimate Process - From the prior to the posterior
GLM prior DESeq LFC
updated 23 months ago by 42k • written 23 months ago by • 0
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5
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1.2k
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Error in DEseq
DEseq RNASeqData
updated 23 months ago by ★ 4.1k • written 23 months ago by • 0
2
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1
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1.5k
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Difference between raw counts and featureCounts for DESeq2
deseq featurecounts counts DESeq2
updated 2.0 years ago by ★ 1.4k • written 2.0 years ago by ▴ 10
1
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5
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1.5k
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Potential outlier/high variance
deseq DESeq2
updated 2.1 years ago by 42k • written 2.1 years ago by • 0
1
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2
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931
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Deseq2 with imbalanced design
Deseq
2.2 years ago Alex • 0
1
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4
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1.6k
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Test if a gene is NOT differentially expressed in DESeq2?
DESeq2 deseq
updated 2.3 years ago by 42k • written 2.3 years ago by • 0
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2
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1.1k
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DESeqDataSet design issue
DESeq DESeq2
2.4 years ago matthew.valentine • 0
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1
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1.5k
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DESeq2 rows did not converge in beta, how to solve
DESeq DESeq2
updated 2.6 years ago by 42k • written 2.6 years ago by • 0
4
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6
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1.7k
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Interpretation of DESeq2 results with 3 factorial design with interaction terms.
r DESeq DESeq2
2.6 years ago s-rhussien • 0
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2
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2.3k
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Correct way to make multiple comparisons on DESeq2?
DESeq DESeq2 R
2.7 years ago jbnrodriguez ▴ 10
1
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2
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998
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DESeq2 log2Foldchanges opposite sign for almost the same groups of comparison
RNASeq DESeq
2.7 years ago krawczyk.margarita • 0
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2
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1.5k
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same padj for all the genes after DEseq analysis
etLRT WALD edgeR DESEq
updated 2.8 years ago by 42k • written 2.8 years ago by • 0
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1
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1.1k
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Filtering DESeq2 results for | LFC | > 1 genes
RNAseq LFC DEseq
3.0 years ago ayy2110 • 0
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2
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960
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metage problem with DESeq
DESeq metagene2 metagene
updated 3.2 years ago by ▴ 10 • written 3.2 years ago by ▴ 10
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3
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2.3k
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Understanding MA plot distortion
DESeq2 MAplot deseq
updated 3.2 years ago by 42k • written 3.2 years ago by • 0
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5
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1.8k
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ZINB-WaVE-DESeq2 with Bulk Data: Choice of Epsilon value, K and gene number
DESeq2 ZINB zinbwave deseq
updated 3.3 years ago by 42k • written 3.3 years ago by • 0
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12
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4.5k
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Deseq2: How to adjust for baseline read counts when testing for groups differences at post-treatment
deseq2 deseq
updated 3.6 years ago by 42k • written 9.0 years ago by • 0
1
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994
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DESeq Error (nbinomTest ())
Deseq nbinomTest
4.0 years ago canfield ▴ 10
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7
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1.9k
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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 4.0 years ago by ★ 3.9k • written 4.0 years ago by • 0
2
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5
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5.7k
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ERROR configuration failed for package RCurl during installation of DESeq
ERROR: configuration failed for package ‘RCurl’ DESeq
written 4.1 years ago by ▴ 10
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2
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876
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Mocking data for understanding interactions in DESeq2
deseq2 deseq
updated 4.1 years ago by ★ 3.7k • written 4.1 years ago by • 0
3
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5
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2.1k
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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 4.1 years ago by 42k • written 4.1 years ago by ▴ 830
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9
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1.3k
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Wrong results of DESeq compared to DESeq2 for some test cases?
deseq2 DESeq
updated 4.2 years ago by ★ 3.7k • written 4.2 years ago by • 0
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7
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1.2k
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how to analyze and find differentially expressed genes based on miRNA gene raw read counts?
deseq2 deseq
4.3 years ago MANYA_BIOINFO • 0
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1.3k
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DESeq2 counts function not working
deseq2 Deseq RNAseq
updated 4.5 years ago by 42k • written 4.5 years ago by ▴ 10
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3
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1.4k
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DESeq2 2x2 factorial design: find genes unique to factor A?
deseq2 deseq differential expression contrasts
updated 4.5 years ago by 42k • written 4.5 years ago by ▴ 180
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4
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4.5k
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TMM Normalization: DESeqDataSet: some values in assay are negative
deseq2 deseq normalization
updated 4.8 years ago by ▴ 40 • written 4.8 years ago by • 0
1
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2
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908
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Filtering extraneous samples affects DESeq results. What is going on?
deseq deseq2
updated 4.8 years ago by 42k • written 4.8 years ago by • 0
0
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0
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958
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Including sva results in SeqGSEA with data with batch effect
limma deseq2 seqgsea sva deseq
4.9 years ago kentfung ▴ 20
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NOOB question: How to use contrasts for subgroup analysis in DESeq2?
deseq deseq2 contrast subgroup
5.2 years ago ariel ▴ 20
3
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12
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1.6k
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Why did I get NA p-values in DESeq with continuous variable?
deseq2 p-value continuous deseq
5.2 years ago ariel ▴ 20
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3
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1.9k
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DESeq2 count outlier replacement from Cook's threshold
deseq2 deseq rnaseq outliers count outliers
updated 5.5 years ago by 42k • written 5.5 years ago by ▴ 10
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1
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1.0k
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Question about multi-factor Deseq analysis
DESeq deseq2 microbiome gut microbiome
updated 5.5 years ago by 42k • written 5.5 years ago by • 0
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3
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1.2k
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Strange lfcShrink plot when running DESeq2 workflow
DESeq2 rnaseq rna-seq deseq2 deseq
5.6 years ago Ben ▴ 50
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7
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3.9k
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DESeq2 install problem
deseq
updated 5.6 years ago by 42k • written 5.6 years ago by • 0
5
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7
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3.6k
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Deseq2 design for one condition over 8 different time point
deseq2 rna-seq design matrix deseq
updated 5.6 years ago by 42k • written 5.6 years ago by ▴ 10
50 results • Page 1 of 1
Recent ...
Replies
Answer: Numerical differences in DESeq2 output depending on different design matrix cons by Michael Love 42k
Yes there can be small numerical differences in the estimated quantities because of how the algorithms decide to stop iterating.
Answer: DESeq2- Mysterious interaction suppresses DEGs by Michael Love 42k
Removing samples from one group nevertheless changes the variance estimation (dispersion) for all comparisons. So you could have pushed one…
Comment: Numerical differences in DESeq2 output depending on different design matrix cons by JKim • 0
The 1st model has an interaction term, but the 2nd model doesn't have the interaction term. That makes the difference.
Comment: Ensembl plants at annotationHub? by Daniele • 0
Hi, I'm using Ensembl Plants release 59 with the IWGSC RefSeq v1.1 gene annotation. Thanks a lot for replying so quickly!
Comment: Numerical differences in DESeq2 output depending on different design matrix cons by swbarnes2 ★ 1.4k
If you restrict yourself to, say, genes with a baseMean > 50, are the numerical differences between the two designs significant?
Votes
Answer: Error while installing BiocManager::install("org.Vdahliae.eg.db")
Comment: How can I create a eigencorplot of pca created from deseq2 object with PCAtools
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
Rsubread counting peaks ATACseq
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