Showing : DEseq • reset
2
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62
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Difference between raw counts and featureCounts for DESeq2
deseq featurecounts counts DESeq2
updated 4 days ago by ★ 1.0k • written 5 days ago by • 0
1
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5
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233
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Potential outlier/high variance
deseq DESeq2
updated 25 days ago by 36k • written 5 weeks ago by • 0
1
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2
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127
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Deseq2 with imbalanced design
Deseq
9 weeks ago Alex • 0
1
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4
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334
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Test if a gene is NOT differentially expressed in DESeq2?
DESeq2 deseq
updated 3 months ago by 36k • written 3 months ago by • 0
0
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2
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240
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DESeqDataSet design issue
DESeq DESeq2
5 months ago matthew.valentine • 0
1
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1
reply
286
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DESeq2 rows did not converge in beta, how to solve
DESeq DESeq2
updated 6 months ago by 36k • written 6 months ago by • 0
4
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6
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511
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Interpretation of DESeq2 results with 3 factorial design with interaction terms.
r DESeq DESeq2
7 months ago s-rhussien • 0
2
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2
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580
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Correct way to make multiple comparisons on DESeq2?
DESeq DESeq2 R
8 months ago jbnrodriguez ▴ 10
1
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2
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291
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DESeq2 log2Foldchanges opposite sign for almost the same groups of comparison
RNASeq DESeq
8 months ago krawczyk.margarita • 0
0
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2
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367
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same padj for all the genes after DEseq analysis
etLRT WALD edgeR DESEq
updated 9 months ago by 36k • written 9 months ago by • 0
0
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1
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246
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Filtering DESeq2 results for | LFC | > 1 genes
RNAseq LFC DEseq
12 months ago ayy2110 • 0
1
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2
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354
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metage problem with DESeq
DESeq metagene2 metagene
updated 14 months ago by ▴ 10 • written 14 months ago by ▴ 10
0
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3
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585
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Understanding MA plot distortion
DESeq2 MAplot deseq
updated 14 months ago by 36k • written 14 months ago by • 0
0
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5
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653
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ZINB-WaVE-DESeq2 with Bulk Data: Choice of Epsilon value, K and gene number
DESeq2 ZINB zinbwave deseq
updated 15 months ago by 36k • written 15 months ago by • 0
1
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12
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2.8k
views
Deseq2: How to adjust for baseline read counts when testing for groups differences at post-treatment
deseq2 deseq
updated 18 months ago by 36k • written 7.0 years ago by • 0
1
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2
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432
views
DESeq Error (nbinomTest ())
Deseq nbinomTest
23 months ago canfield ▴ 10
0
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7
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389
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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 24 months ago by 3.5k • written 24 months ago by • 0
2
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4
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985
views
ERROR configuration failed for package RCurl during installation of DESeq
ERROR: configuration failed for package ‘RCurl’ DESeq
updated 3 months ago by • 0 • written 2.1 years ago by ▴ 10
1
vote
2
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268
views
Mocking data for understanding interactions in DESeq2
deseq2 deseq
updated 2.1 years ago by ★ 3.7k • written 2.1 years ago by • 0
3
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5
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536
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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 2.1 years ago by 36k • written 2.1 years ago by ▴ 780
1
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9
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492
views
Wrong results of DESeq compared to DESeq2 for some test cases?
deseq2 DESeq
updated 2.2 years ago by ★ 3.7k • written 2.2 years ago by • 0
0
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7
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463
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how to analyze and find differentially expressed genes based on miRNA gene raw read counts?
deseq2 deseq
2.3 years ago MANYA_BIOINFO • 0
0
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1
reply
498
views
DESeq2 counts function not working
deseq2 Deseq RNAseq
updated 2.5 years ago by 36k • written 2.5 years ago by ▴ 10
2
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3
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597
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DESeq2 2x2 factorial design: find genes unique to factor A?
deseq2 deseq differential expression contrasts
updated 2.5 years ago by 36k • written 2.5 years ago by ▴ 150
4
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4
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1.5k
views
TMM Normalization: DESeqDataSet: some values in assay are negative
deseq2 deseq normalization
updated 2.8 years ago by ▴ 30 • written 2.8 years ago by • 0
1
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2
replies
410
views
Filtering extraneous samples affects DESeq results. What is going on?
deseq deseq2
updated 2.8 years ago by 36k • written 2.8 years ago by • 0
0
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0
replies
471
views
Including sva results in SeqGSEA with data with batch effect
limma deseq2 seqgsea sva deseq
2.9 years ago kentfung • 0
0
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9
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828
views
NOOB question: How to use contrasts for subgroup analysis in DESeq2?
deseq deseq2 contrast subgroup
3.2 years ago ariel ▴ 10
3
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12
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748
views
Why did I get NA p-values in DESeq with continuous variable?
deseq2 p-value continuous deseq
3.2 years ago ariel ▴ 10
2
votes
3
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1000
views
DESeq2 count outlier replacement from Cook's threshold
deseq2 deseq rnaseq outliers count outliers
updated 3.5 years ago by 36k • written 3.5 years ago by ▴ 10
0
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1
reply
471
views
Question about multi-factor Deseq analysis
DESeq deseq2 microbiome gut microbiome
updated 3.5 years ago by 36k • written 3.5 years ago by • 0
0
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3
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607
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Strange lfcShrink plot when running DESeq2 workflow
DESeq2 rnaseq rna-seq deseq2 deseq
3.6 years ago Ben ▴ 50
0
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7
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2.9k
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DESeq2 install problem
deseq
updated 3.6 years ago by 36k • written 3.6 years ago by • 0
4
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7
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2.0k
views
Deseq2 design for one condition over 8 different time point
deseq2 rna-seq design matrix deseq
updated 3.6 years ago by 36k • written 3.6 years ago by • 0
0
votes
3
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544
views
DESeq2 group comparison
deseq2 deseq differential binding analysis
updated 3.7 years ago by 36k • written 3.7 years ago by ▴ 60
3
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5
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634
views
Help with multi-factor Deseq analysis
deseq2 rnaseq deseq
updated 3.7 years ago by 36k • written 3.7 years ago by • 0
0
votes
7
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663
views
Deseq 2 multiple comparisons (3 groups, 24 samples)
deseq
updated 3.7 years ago by 36k • written 3.7 years ago by • 0
4
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1
reply
13k
views
The latest version of R is 3.5.1 and it is not compatible with many Bioconductor packages.
R deseq tcgabiolinks
3.7 years ago ansari.sarabio • 0
1
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5
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561
views
Group Specific Condition Query
deseq2 deseq batcheffect
updated 3.8 years ago by 36k • written 3.8 years ago by • 0
3
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7
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594
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The discrepancy between the mean of extracted fitted value and calculated mean and SE based on LFC.
deseq2 deseq
3.8 years ago blastzone.heimerdinger ▴ 10
0
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8
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1.1k
views
DESeq2 Multi factor, multi time point comparison design formula
rna-seq deseq2 deseq R
updated 3.8 years ago by 36k • written 3.8 years ago by • 0
0
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1
reply
434
views
how to start normalization
deseq
3.8 years ago raghavaraghava049 • 0
0
votes
1
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498
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Basemean always multiples of 0.5 in deseq2 results
deseq results baseMean
updated 3.8 years ago by 36k • written 3.9 years ago by • 0
0
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3
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482
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3x2 comparisons in DEseq - time (3 time points) and two treatments
deseq2 deseq rna-seq multiple comparisons
updated 3.9 years ago by 36k • written 3.9 years ago by ▴ 60
2
votes
3
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842
views
ASE using DESeq2
deseq2 deseq normalization allele specific expression rnaseq
updated 4.0 years ago by ★ 3.7k • written 4.0 years ago by • 0
0
votes
5
replies
696
views
How to simulate time course RNA seq data using DESeq?
deseq2 R makeexampledeseqdataset deseq
updated 4.0 years ago by 36k • written 4.0 years ago by • 0
3
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7
replies
1.3k
views
novice: building gene co-expression network using RNA-Seq data
rna-seq WGCNA deseq method coexpression
updated 4.1 years ago by ★ 2.6k • written 4.1 years ago by ▴ 10
1
vote
2
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870
views
Deseq2 with replicate mean and variance information
deseq2 deseq differential analysis proteomics
4.1 years ago blehtine • 0
1
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8
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1.5k
views
DESeq2 : group specific effect of a treatment while controlling for individual effect
deseq2 DESeq design and contrast matrix deseq
4.2 years ago SPbeginner • 0
1
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3
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712
views
DEseq2 sample imbalance
deseq
4.2 years ago aishu.jp ▴ 20
50 results • Page 1 of 1
Recent ...
Replies
Comment: Warnings when using "ashr" in lfcshrinkage for DESeq2 by andrebolerbarros ▴ 10
Hi Michael, I'm using the "contrast" parameter, so I cannot use apeglm with that, as far as I know. The "coef" will not allow me to do eve…
Comment: Transcript-level differential expression using DESeq2 by Michael Love 36k
So the way the p-values are generated (non-parametric) you won't get a ranking among these that are highly significant. You can use logFC. …
Answer: Warnings when using "ashr" in lfcshrinkage for DESeq2 by Michael Love 36k
Note sure why it's having difficulty converging. You could use apeglm?
Comment: performing the differential binding in ChIP-seq by ATpoint ★ 1.2k
Cross-posted https://www.biostars.org/p/9524012/#9524012
Comment: Transcript-level differential expression using DESeq2 by Ekta • 0
Yes, i tried that. I used salmon bootstraps also for the same RNAseq data to run Swish and performed the Differential transcript expressio…
Votes
Answer: how to make a group to apply the data to CAMERA
Answer: how to make a group to apply the data to CAMERA
Comment: Using vegan::betadisper for determing if I subset my design for DESeq2
Answer: How to best visualize multi-level transcriptomics experiment data?
A: Interpreting results of sample-to-sample PCA/clustering and changing assignment
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