Showing : DESeq • reset
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DESeq2 "Not full rank" and "less than full rank" error
DESeq2 deseq
updated 13 months ago by ★ 4.1k • written 13 months ago by • 0
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866
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evaluate the variable importance on genes
DESeq2 deseq
21 months ago Meme • 0
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2
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824
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Running DESeq on normalized data
deseq DESeq2
updated 24 months ago by ★ 5.0k • written 24 months ago by • 0
2
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2
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1.2k
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Predicting missing values splines DESeq2
deseq DESeq2
2.1 years ago georgii.vdovin • 0
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838
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Controling for Covariates With a Continuous Predictor Variable
Deseq DESeq2
updated 2.1 years ago by 43k • written 2.1 years ago by • 0
1
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1
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1.6k
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Can I transform already normalized rna-seq data with Z-score?
Z-score RNASeqData Deseq DESeq2
updated 2.2 years ago by 68k • written 2.2 years ago by • 0
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3
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4.1k
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Difference between DESeqDataSetFromMatrix() function and DESeq() function
DESeq DESeq2
updated 2.4 years ago by ★ 5.0k • written 2.4 years ago by ▴ 10
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4
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1.4k
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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 2.4 years ago by 43k • written 2.4 years ago by ▴ 20
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2
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1.3k
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summarizeToGene in tximeta causing vastly different results
DESeq2 deseq txime tximeta
updated 2.6 years ago by 43k • written 2.6 years ago by • 0
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4
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2.7k
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Volcano plot becomes flipped when I add a third condition
DESeq2 volcanoplot deseq HELP contrast
updated 2.8 years ago by ▴ 780 • written 2.8 years ago by • 0
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962
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What is the difference between these two arguments for log fold change shrinkage?
DESeq
updated 2.9 years ago by 43k • written 2.9 years ago by ▴ 10
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1.2k
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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 2.9 years ago by ★ 1.6k • written 2.9 years ago by ▴ 10
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1.7k
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suggestions/comments on DESeq transcript wise analysis
convert DESeq convert DESeq
written 13.8 years ago by ▴ 190
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1
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891
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How to design multifactor DESEQ2 formula?
DESEQ DESEQ2
updated 3.3 years ago by ★ 5.0k • written 3.3 years ago by • 0
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2
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1.4k
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DESeq2 is renaming gene names and lack of downregulated genes
DESeq DESeq2
3.4 years ago manwar • 0
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1
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1.3k
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Gene wise dispersion estimate Process - From the prior to the posterior
GLM prior DESeq LFC
updated 3.5 years ago by 43k • written 3.5 years ago by • 0
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5
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1.9k
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Error in DEseq
DEseq RNASeqData
updated 3.5 years ago by ★ 5.0k • written 3.5 years ago by • 0
2
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1
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2.3k
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Difference between raw counts and featureCounts for DESeq2
deseq featurecounts counts DESeq2
updated 3.6 years ago by ★ 1.4k • written 3.6 years ago by ▴ 10
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5
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2.1k
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Potential outlier/high variance
deseq DESeq2
updated 3.6 years ago by 43k • written 3.7 years ago by • 0
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2
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1.4k
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Deseq2 with imbalanced design
Deseq
3.7 years ago Alex • 0
1
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4
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2.5k
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Test if a gene is NOT differentially expressed in DESeq2?
DESeq2 deseq
updated 3.9 years ago by 43k • written 3.9 years ago by • 0
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2
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1.8k
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DESeqDataSet design issue
DESeq DESeq2
4.0 years ago matthew.valentine • 0
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1
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2.3k
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DESeq2 rows did not converge in beta, how to solve
DESeq DESeq2
updated 4.1 years ago by 43k • written 4.1 years ago by • 0
4
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6
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2.6k
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Interpretation of DESeq2 results with 3 factorial design with interaction terms.
r DESeq DESeq2
4.2 years ago s-rhussien • 0
2
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2
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2.9k
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Correct way to make multiple comparisons on DESeq2?
DESeq DESeq2 R
4.3 years ago • updated 4.2 years ago jbnrodriguez ▴ 10
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2
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1.4k
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DESeq2 log2Foldchanges opposite sign for almost the same groups of comparison
RNASeq DESeq
4.3 years ago krawczyk.margarita • 0
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2.3k
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same padj for all the genes after DEseq analysis
etLRT WALD edgeR DESEq
updated 4.3 years ago by 43k • written 4.3 years ago by • 0
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1
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1.7k
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Filtering DESeq2 results for | LFC | > 1 genes
RNAseq LFC DEseq
4.5 years ago ayy2110 • 0
1
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2
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1.5k
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metage problem with DESeq
DESeq metagene2 metagene
updated 4.7 years ago by ▴ 10 • written 4.8 years ago by ▴ 10
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3
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3.9k
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Understanding MA plot distortion
DESeq2 MAplot deseq
updated 4.8 years ago by 43k • written 4.8 years ago by • 0
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5
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2.6k
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ZINB-WaVE-DESeq2 with Bulk Data: Choice of Epsilon value, K and gene number
DESeq2 ZINB zinbwave deseq
updated 4.8 years ago by 43k • written 4.8 years ago by • 0
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12
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5.7k
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Deseq2: How to adjust for baseline read counts when testing for groups differences at post-treatment
deseq2 deseq
updated 5.1 years ago by 43k • written 10.6 years ago by • 0
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2
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1.4k
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DESeq Error (nbinomTest ())
Deseq nbinomTest
5.5 years ago canfield ▴ 10
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7
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2.8k
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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 5.5 years ago by ★ 4.0k • written 5.5 years ago by • 0
2
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5
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7.4k
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ERROR configuration failed for package RCurl during installation of DESeq
ERROR: configuration failed for package ‘RCurl’ DESeq
written 5.7 years ago by ▴ 10
2
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2
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1.4k
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Mocking data for understanding interactions in DESeq2
deseq2 deseq
updated 5.7 years ago by ★ 3.8k • written 5.7 years ago by • 0
3
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5
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3.1k
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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 5.7 years ago by 43k • written 5.7 years ago by ▴ 840
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9
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2.0k
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Wrong results of DESeq compared to DESeq2 for some test cases?
deseq2 DESeq
updated 5.7 years ago by ★ 3.8k • written 5.7 years ago by • 0
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7
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1.9k
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how to analyze and find differentially expressed genes based on miRNA gene raw read counts?
deseq2 deseq
5.9 years ago MANYA_BIOINFO • 0
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1
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1.9k
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DESeq2 counts function not working
deseq2 Deseq RNAseq
updated 6.0 years ago by 43k • written 6.0 years ago by ▴ 10
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3
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1.9k
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DESeq2 2x2 factorial design: find genes unique to factor A?
deseq2 deseq differential expression contrasts
updated 6.1 years ago by 43k • written 6.1 years ago by ▴ 180
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4
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6.1k
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TMM Normalization: DESeqDataSet: some values in assay are negative
deseq2 deseq normalization
updated 6.4 years ago by ▴ 40 • written 6.4 years ago by • 0
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2
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1.3k
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Filtering extraneous samples affects DESeq results. What is going on?
deseq deseq2
updated 6.4 years ago by 43k • written 6.4 years ago by • 0
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0
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1.4k
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Including sva results in SeqGSEA with data with batch effect
limma deseq2 seqgsea sva deseq
6.4 years ago kentfung ▴ 20
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9
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2.9k
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NOOB question: How to use contrasts for subgroup analysis in DESeq2?
deseq deseq2 contrast subgroup
6.8 years ago ariel ▴ 20
3
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12
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2.4k
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Why did I get NA p-values in DESeq with continuous variable?
deseq2 p-value continuous deseq
6.8 years ago ariel ▴ 20
2
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3
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2.6k
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DESeq2 count outlier replacement from Cook's threshold
deseq2 deseq rnaseq outliers count outliers
updated 7.0 years ago by 43k • written 7.0 years ago by ▴ 10
0
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1
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1.4k
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Question about multi-factor Deseq analysis
DESeq deseq2 microbiome gut microbiome
updated 7.1 years ago by 43k • written 7.1 years ago by • 0
0
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3
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1.7k
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Strange lfcShrink plot when running DESeq2 workflow
DESeq2 rnaseq rna-seq deseq2 deseq
7.2 years ago Ben ▴ 50
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7
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4.5k
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DESeq2 install problem
deseq
updated 7.2 years ago by 43k • written 7.2 years ago by • 0
512 results • Page 1 of 11
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Comment: DECIPHER DesignProbes unable to design FISH-probes by Erik Wright ▴ 150
Are the sequences aligned (i.e., the same width) before running `TileSeqs()`?
Comment: BiocParallel (and DESeq2) - wrong args for environment subassignment by Michael Love 43k
BTW, I tested with no issue on MacOS ARM on our previous github issue.
Answer: DESeq(dds, parallel=TRUE) wrong args for environment subassignment by Michael Love 43k
The DESeq2 error makes sense, as we've talked about, given that the simple `bplapply` isn't working in your setup. Maybe give the traceb…
Answer: PTM analysis in LIMPA by Gordon Smyth 53k
For PTM analysis, the usual quantification command dpcQuant() is replaced by dpcImpute(). Otherwise the limpa pipeline is the same as for a…
Answer: problem reading bam files into nucleR by James W. MacDonald 68k
The first step is to update to the current versions of R/Bioconductor and try again. It's possible that you have run into a bug that's alre…
Votes
C: DESeq2 Following RSEM
Upcoming Ensembl API and data access changes - new blog post available
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
Awards • All
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Popular Question to James W. MacDonald 68k
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