Showing : DEseq • reset
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What is the difference between these two arguments for log fold change shrinkage?
DESeq
updated 1 day ago by ★ 2.1k • written 1 day ago by • 0
0
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1
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105
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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 10 days ago by ★ 1.5k • written 11 days ago by • 0
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2
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759
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suggestions/comments on DESeq transcript wise analysis
convert DESeq convert DESeq
written 11.0 years ago by ▴ 190
1
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1
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173
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How to design multifactor DESEQ2 formula?
DESEQ DESEQ2
updated 4 months ago by ★ 2.1k • written 4 months ago by • 0
3
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2
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286
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DESeq2 is renaming gene names and lack of downregulated genes
DESeq DESeq2
6 months ago manwar • 0
1
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1
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278
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Gene wise dispersion estimate Process - From the prior to the posterior
GLM prior DESeq LFC
updated 7 months ago by 39k • written 7 months ago by • 0
1
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5
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405
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Error in DEseq
DEseq RNASeqData
updated 7 months ago by ★ 2.1k • written 7 months ago by • 0
2
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1
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444
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Difference between raw counts and featureCounts for DESeq2
deseq featurecounts counts DESeq2
updated 8 months ago by ★ 1.2k • written 8 months ago by • 0
1
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5
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584
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Potential outlier/high variance
deseq DESeq2
updated 9 months ago by 39k • written 9 months ago by • 0
1
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2
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330
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Deseq2 with imbalanced design
Deseq
10 months ago Alex • 0
1
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4
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659
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Test if a gene is NOT differentially expressed in DESeq2?
DESeq2 deseq
updated 12 months ago by 39k • written 12 months ago by • 0
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2
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479
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DESeqDataSet design issue
DESeq DESeq2
13 months ago matthew.valentine • 0
1
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1
reply
591
views
DESeq2 rows did not converge in beta, how to solve
DESeq DESeq2
updated 15 months ago by 39k • written 15 months ago by • 0
4
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6
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858
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Interpretation of DESeq2 results with 3 factorial design with interaction terms.
r DESeq DESeq2
16 months ago s-rhussien • 0
2
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2
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1.1k
views
Correct way to make multiple comparisons on DESeq2?
DESeq DESeq2 R
17 months ago • updated 16 months ago jbnrodriguez ▴ 10
1
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2
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448
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DESeq2 log2Foldchanges opposite sign for almost the same groups of comparison
RNASeq DESeq
17 months ago krawczyk.margarita • 0
0
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2
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671
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same padj for all the genes after DEseq analysis
etLRT WALD edgeR DESEq
updated 17 months ago by 39k • written 17 months ago by • 0
0
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1
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480
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Filtering DESeq2 results for | LFC | > 1 genes
RNAseq LFC DEseq
20 months ago ayy2110 • 0
1
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2
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534
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metage problem with DESeq
DESeq metagene2 metagene
updated 22 months ago by ▴ 10 • written 23 months ago by ▴ 10
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3
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1.1k
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Understanding MA plot distortion
DESeq2 MAplot deseq
updated 23 months ago by 39k • written 23 months ago by • 0
0
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5
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951
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ZINB-WaVE-DESeq2 with Bulk Data: Choice of Epsilon value, K and gene number
DESeq2 ZINB zinbwave deseq
updated 24 months ago by 39k • written 24 months ago by • 0
2
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12
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3.2k
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Deseq2: How to adjust for baseline read counts when testing for groups differences at post-treatment
deseq2 deseq
updated 2.2 years ago by 39k • written 7.7 years ago by • 0
1
vote
2
replies
572
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DESeq Error (nbinomTest ())
Deseq nbinomTest
2.6 years ago canfield ▴ 10
0
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7
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730
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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 2.7 years ago by 3.7k • written 2.7 years ago by • 0
2
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4
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2.4k
views
ERROR configuration failed for package RCurl during installation of DESeq
ERROR: configuration failed for package ‘RCurl’ DESeq
updated 11 months ago by • 0 • written 2.8 years ago by ▴ 10
1
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2
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376
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Mocking data for understanding interactions in DESeq2
deseq2 deseq
updated 2.8 years ago by ★ 3.7k • written 2.8 years ago by • 0
3
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5
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1.0k
views
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 2.8 years ago by 39k • written 2.8 years ago by ▴ 800
1
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9
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659
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Wrong results of DESeq compared to DESeq2 for some test cases?
deseq2 DESeq
updated 2.9 years ago by ★ 3.7k • written 2.9 years ago by • 0
0
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7
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584
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how to analyze and find differentially expressed genes based on miRNA gene raw read counts?
deseq2 deseq
3.0 years ago MANYA_BIOINFO • 0
0
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1
reply
679
views
DESeq2 counts function not working
deseq2 Deseq RNAseq
updated 3.1 years ago by 39k • written 3.1 years ago by ▴ 10
2
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3
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807
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DESeq2 2x2 factorial design: find genes unique to factor A?
deseq2 deseq differential expression contrasts
updated 3.2 years ago by 39k • written 3.2 years ago by ▴ 180
4
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4
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2.3k
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TMM Normalization: DESeqDataSet: some values in assay are negative
deseq2 deseq normalization
updated 3.5 years ago by ▴ 30 • written 3.5 years ago by • 0
1
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2
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515
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Filtering extraneous samples affects DESeq results. What is going on?
deseq deseq2
updated 3.5 years ago by 39k • written 3.5 years ago by • 0
0
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0
replies
596
views
Including sva results in SeqGSEA with data with batch effect
limma deseq2 seqgsea sva deseq
3.6 years ago kentfung ▴ 10
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9
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1.1k
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NOOB question: How to use contrasts for subgroup analysis in DESeq2?
deseq deseq2 contrast subgroup
3.9 years ago ariel ▴ 10
3
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12
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912
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Why did I get NA p-values in DESeq with continuous variable?
deseq2 p-value continuous deseq
3.9 years ago ariel ▴ 10
2
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3
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1.2k
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DESeq2 count outlier replacement from Cook's threshold
deseq2 deseq rnaseq outliers count outliers
updated 4.1 years ago by 39k • written 4.1 years ago by ▴ 10
0
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1
reply
595
views
Question about multi-factor Deseq analysis
DESeq deseq2 microbiome gut microbiome
updated 4.2 years ago by 39k • written 4.2 years ago by • 0
0
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3
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729
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Strange lfcShrink plot when running DESeq2 workflow
DESeq2 rnaseq rna-seq deseq2 deseq
4.3 years ago Ben ▴ 50
0
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7
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3.3k
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DESeq2 install problem
deseq
updated 4.3 years ago by 39k • written 4.3 years ago by • 0
4
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7
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2.4k
views
Deseq2 design for one condition over 8 different time point
deseq2 rna-seq design matrix deseq
updated 4.3 years ago by 39k • written 4.3 years ago by • 0
0
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3
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658
views
DESeq2 group comparison
deseq2 deseq differential binding analysis
updated 4.3 years ago by 39k • written 4.3 years ago by ▴ 60
3
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5
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725
views
Help with multi-factor Deseq analysis
deseq2 rnaseq deseq
updated 4.4 years ago by 39k • written 4.4 years ago by • 0
0
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7
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774
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Deseq 2 multiple comparisons (3 groups, 24 samples)
deseq
updated 4.4 years ago by 39k • written 4.4 years ago by • 0
4
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1
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13k
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The latest version of R is 3.5.1 and it is not compatible with many Bioconductor packages.
R deseq tcgabiolinks
4.4 years ago ansari.sarabio • 0
1
vote
5
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696
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Group Specific Condition Query
deseq2 deseq batcheffect
updated 4.4 years ago by 39k • written 4.4 years ago by • 0
3
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7
replies
710
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The discrepancy between the mean of extracted fitted value and calculated mean and SE based on LFC.
deseq2 deseq
4.5 years ago blastzone.heimerdinger ▴ 10
0
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8
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1.4k
views
DESeq2 Multi factor, multi time point comparison design formula
rna-seq deseq2 deseq R
updated 4.5 years ago by 39k • written 4.5 years ago by • 0
0
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1
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512
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how to start normalization
deseq
4.5 years ago raghavaraghava049 • 0
0
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1
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611
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Basemean always multiples of 0.5 in deseq2 results
deseq results baseMean
updated 4.5 years ago by 39k • written 4.5 years ago by • 0
50 results • Page 1 of 1
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Comment: edgeR: Usage of estimated dispersion from replicates for pools of the same exper by k.roelfs • 0
I felt that my way of analyzing this data set was a bit unfortunate. I was not involved in the experimental design myself and am now trying…
Comment: edgeR: Usage of estimated dispersion from replicates for pools of the same exper by k.roelfs • 0
For tissue T1 and each time point, each replicate corresponds to a single plant. For tissue T2, we actually had to sample 5 plants per rep…
Answer: edgeR: Usage of estimated dispersion from replicates for pools of the same exper by Gordon Smyth 47k
> Due to the high degree of heterozygosity of the plants used for the experiment, we thought it best to pool the same tissue under the same…
Comment: edgeR: Usage of estimated dispersion from replicates for pools of the same exper by Gordon Smyth 47k
How many plants are used for each of the biological replicate samples? One plant or a few?
Comment: edgeR: Usage of estimated dispersion from replicates for pools of the same exper by k.roelfs • 0
Yes you are right, we have 24 RNA-seq libraries in total. The replicates come from the same population of plants, but independent from tho…
Votes
DESeq2 pairwise comparisons w/ 3 factors
A: DESeq2 pairwise comparisons w/ 3 factors
A: DESeq2 pairwise comparisons w/ 3 factors
Comment: MA plot
Comment: MA plot
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