Showing : DEseq • reset
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DESeq2 "Not full rank" and "less than full rank" error
DESeq2 deseq
updated 7 weeks ago by ★ 4.1k • written 7 weeks ago by • 0
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2
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600
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evaluate the variable importance on genes
DESeq2 deseq
10 months ago Meme • 0
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2
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552
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Running DESeq on normalized data
deseq DESeq2
updated 12 months ago by ★ 4.6k • written 12 months ago by • 0
2
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2
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810
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Predicting missing values splines DESeq2
deseq DESeq2
13 months ago georgii.vdovin • 0
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591
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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
1
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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 15 months ago by 67k • written 15 months ago by • 0
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3
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2.5k
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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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955
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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 17 months ago by 43k • written 17 months ago by ▴ 20
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2
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942
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summarizeToGene in tximeta causing vastly different results
DESeq2 deseq txime tximeta
updated 20 months ago by 43k • written 20 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 22 months ago by ▴ 780 • written 22 months ago by • 0
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1
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756
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What is the difference between these two arguments for log fold change shrinkage?
DESeq
updated 23 months ago by 43k • written 23 months ago by ▴ 10
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1
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976
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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 23 months ago by ★ 1.5k • written 23 months ago by ▴ 10
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2
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1.5k
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suggestions/comments on DESeq transcript wise analysis
convert DESeq convert DESeq
written 12.9 years ago by ▴ 190
1
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1
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685
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How to design multifactor DESEQ2 formula?
DESEQ DESEQ2
updated 2.3 years ago by ★ 4.6k • written 2.3 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
2.4 years ago manwar • 0
1
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1
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1000
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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 2.6 years ago by ★ 1.4k • written 2.6 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 2.7 years ago by • 0
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2
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1.1k
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Deseq2 with imbalanced design
Deseq
2.8 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 2.9 years ago by 43k • written 2.9 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
4
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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
2
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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
3.3 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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1.3k
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Filtering DESeq2 results for | LFC | > 1 genes
RNAseq LFC DEseq
3.6 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 3.8 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 3.8 years ago by 43k • written 3.8 years ago by • 0
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 3.9 years ago by 43k • written 3.9 years ago by • 0
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12
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5.0k
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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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2.3k
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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 4.6 years ago by ★ 4.0k • written 4.6 years ago by • 0
2
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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 4.7 years ago by ▴ 10
2
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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 4.7 years ago by ★ 3.8k • written 4.7 years ago by • 0
3
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5
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2.5k
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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
4.9 years ago MANYA_BIOINFO • 0
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1
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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 5.1 years ago by 43k • written 5.1 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 5.4 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 5.4 years ago by 43k • written 5.4 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
3
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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
2
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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
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
6.2 years ago Ben ▴ 50
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7
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4.2k
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DESeq2 install problem
deseq
updated 6.2 years ago by 43k • written 6.2 years ago by • 0
50 results • Page 1 of 1
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Comment: Incorporating Salmon offset matrix into Wilcoxon DEG analysis by Gordon Smyth 52k
It is not possible to use both. estimateGLMRobustDisp() estimates negative binomial dispersions for each gene, whereas glmQLFit() estimates…
Comment: Incorporating Salmon offset matrix into Wilcoxon DEG analysis by Andre • 0
Thank you. What is the difference between setting robust=TRUE in glmQLFit and estimateGLMRobustDisp? The paper i mentioned in the post used…
Comment: PCA of different bacterial species by Jeremy • 0
Your approach of using ~2500 single-copy orthologs and normalizing with VST or rlog for PCA is valid for exploring general clustering [pap…
Comment: RnBeads::combine() - error? by Urotree • 0
pheno <- rnb.set.arrays@pheno # Phenotypic data sites <- rnb.set.arrays@sites # CpG site definitions (data.frame) meth <- rnb.set…
Comment: RnBeads::combine() - error? by Urotree • 0
![enter image description here][1] [1]: /media/images/40d9778d-b044-4405-9b3d-2ba835f6 Hi, after I convert to RnBiseqSet, it shows "All…
Votes
C: How does edgeR cpm function calculate log(CPM) values?
C: How does edgeR cpm function calculate log(CPM) values?
Answer: Incorporating Salmon offset matrix into Wilcoxon DEG analysis
scater/scran with TPMs from Salmon - counts?
A: Full length single-cell RNA-seq - tximport output for downstream analysis
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