Showing : DEseq • reset
0
votes
1
reply
680
views
DESeq2 "Not full rank" and "less than full rank" error
DESeq2 deseq
updated 14 months ago by ★ 4.1k • written 14 months ago by • 0
1
vote
2
replies
900
views
evaluate the variable importance on genes
DESeq2 deseq
23 months ago Meme • 0
0
votes
2
replies
861
views
Running DESeq on normalized data
deseq DESeq2
updated 2.1 years ago by ★ 5.0k • written 2.1 years ago by • 0
2
votes
2
replies
1.2k
views
Predicting missing values splines DESeq2
deseq DESeq2
2.2 years ago georgii.vdovin • 0
0
votes
1
reply
858
views
Controling for Covariates With a Continuous Predictor Variable
Deseq DESeq2
updated 2.2 years ago by 43k • written 2.2 years ago by • 0
1
vote
1
reply
1.7k
views
Can I transform already normalized rna-seq data with Z-score?
Z-score RNASeqData Deseq DESeq2
updated 2.3 years ago by 68k • written 2.3 years ago by • 0
0
votes
3
replies
4.3k
views
Difference between DESeqDataSetFromMatrix() function and DESeq() function
DESeq DESeq2
updated 2.5 years ago by ★ 5.0k • written 2.5 years ago by ▴ 10
0
votes
4
replies
1.4k
views
lfc direction of effect flipped for ashr, apeGLM, but accurate to biological data for non-shrunken
DESeq2 apeglm DESeq ApeGLM Ashr
updated 2.5 years ago by 43k • written 2.5 years ago by ▴ 20
1
vote
2
replies
1.3k
views
summarizeToGene in tximeta causing vastly different results
DESeq2 deseq txime tximeta
updated 2.7 years ago by 43k • written 2.7 years ago by • 0
0
votes
4
replies
2.7k
views
Volcano plot becomes flipped when I add a third condition
DESeq2 volcanoplot deseq HELP contrast
updated 2.9 years ago by ▴ 780 • written 2.9 years ago by • 0
0
votes
1
reply
987
views
What is the difference between these two arguments for log fold change shrinkage?
DESeq
updated 3.0 years ago by 43k • written 3.0 years ago by ▴ 10
0
votes
1
reply
1.3k
views
Is it possible to convert transcript-level to gene-level dataset to use it in DESeq2 ?
DESeq2 Transcriptomics tximport deseq txi
updated 3.0 years ago by ★ 1.6k • written 3.0 years ago by ▴ 10
0
votes
2
replies
1.7k
views
suggestions/comments on DESeq transcript wise analysis
convert DESeq convert DESeq
written 13.9 years ago by ▴ 190
1
vote
1
reply
924
views
How to design multifactor DESEQ2 formula?
DESEQ DESEQ2
updated 3.4 years ago by ★ 5.0k • written 3.4 years ago by • 0
3
votes
2
replies
1.5k
views
DESeq2 is renaming gene names and lack of downregulated genes
DESeq DESeq2
3.5 years ago manwar • 0
1
vote
1
reply
1.3k
views
Gene wise dispersion estimate Process - From the prior to the posterior
GLM prior DESeq LFC
updated 3.6 years ago by 43k • written 3.6 years ago by • 0
1
vote
5
replies
1.9k
views
Error in DEseq
DEseq RNASeqData
updated 3.6 years ago by ★ 5.0k • written 3.6 years ago by • 0
2
votes
1
reply
2.4k
views
Difference between raw counts and featureCounts for DESeq2
deseq featurecounts counts DESeq2
updated 3.7 years ago by ★ 1.4k • written 3.7 years ago by ▴ 10
1
vote
5
replies
2.2k
views
Potential outlier/high variance
deseq DESeq2
updated 3.7 years ago by 43k • written 3.8 years ago by • 0
1
vote
2
replies
1.5k
views
Deseq2 with imbalanced design
Deseq
3.8 years ago Alex • 0
1
vote
4
replies
2.6k
views
Test if a gene is NOT differentially expressed in DESeq2?
DESeq2 deseq
updated 4.0 years ago by 43k • written 4.0 years ago by • 0
0
votes
2
replies
1.8k
views
DESeqDataSet design issue
DESeq DESeq2
4.1 years ago matthew.valentine • 0
1
vote
1
reply
2.4k
views
DESeq2 rows did not converge in beta, how to solve
DESeq DESeq2
updated 4.2 years ago by 43k • written 4.2 years ago by • 0
4
votes
6
replies
2.7k
views
Interpretation of DESeq2 results with 3 factorial design with interaction terms.
r DESeq DESeq2
4.3 years ago s-rhussien • 0
2
votes
2
replies
2.9k
views
Correct way to make multiple comparisons on DESeq2?
DESeq DESeq2 R
4.4 years ago • updated 4.3 years ago jbnrodriguez ▴ 10
1
vote
2
replies
1.5k
views
DESeq2 log2Foldchanges opposite sign for almost the same groups of comparison
RNASeq DESeq
4.4 years ago krawczyk.margarita • 0
0
votes
2
replies
2.3k
views
same padj for all the genes after DEseq analysis
etLRT WALD edgeR DESEq
updated 4.4 years ago by 43k • written 4.4 years ago by • 0
0
votes
1
reply
1.8k
views
Filtering DESeq2 results for | LFC | > 1 genes
RNAseq LFC DEseq
4.6 years ago ayy2110 • 0
1
vote
2
replies
1.5k
views
metage problem with DESeq
DESeq metagene2 metagene
updated 4.8 years ago by ▴ 10 • written 4.9 years ago by ▴ 10
0
votes
3
replies
4.0k
views
Understanding MA plot distortion
DESeq2 MAplot deseq
updated 4.9 years ago by 43k • written 4.9 years ago by • 0
0
votes
5
replies
2.7k
views
ZINB-WaVE-DESeq2 with Bulk Data: Choice of Epsilon value, K and gene number
DESeq2 ZINB zinbwave deseq
updated 5.0 years ago by 43k • written 5.0 years ago by • 0
2
votes
12
replies
5.9k
views
Deseq2: How to adjust for baseline read counts when testing for groups differences at post-treatment
deseq2 deseq
updated 5.2 years ago by 43k • written 10.7 years ago by • 0
1
vote
2
replies
1.4k
views
DESeq Error (nbinomTest ())
Deseq nbinomTest
5.6 years ago canfield ▴ 10
0
votes
7
replies
2.9k
views
DESeq error: Error in validityMethod(object) : nrow(design) == ncol(object) is not TRUE
deseq2 DESeq nrow == ncol is not TRUE
updated 5.6 years ago by ★ 4.0k • written 5.6 years ago by • 0
2
votes
5
replies
7.5k
views
ERROR configuration failed for package RCurl during installation of DESeq
ERROR: configuration failed for package ‘RCurl’ DESeq
written 5.8 years ago by ▴ 10
2
votes
2
replies
1.5k
views
Mocking data for understanding interactions in DESeq2
deseq2 deseq
updated 5.8 years ago by ★ 3.8k • written 5.8 years ago by • 0
3
votes
5
replies
3.2k
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 5.8 years ago by 43k • written 5.8 years ago by ▴ 840
1
vote
9
replies
2.1k
views
Wrong results of DESeq compared to DESeq2 for some test cases?
deseq2 DESeq
updated 5.8 years ago by ★ 3.8k • written 5.8 years ago by • 0
0
votes
7
replies
2.0k
views
how to analyze and find differentially expressed genes based on miRNA gene raw read counts?
deseq2 deseq
6.0 years ago MANYA_BIOINFO • 0
0
votes
1
reply
2.0k
views
DESeq2 counts function not working
deseq2 Deseq RNAseq
updated 6.1 years ago by 43k • written 6.1 years ago by ▴ 10
2
votes
3
replies
2.0k
views
DESeq2 2x2 factorial design: find genes unique to factor A?
deseq2 deseq differential expression contrasts
updated 6.2 years ago by 43k • written 6.2 years ago by ▴ 180
4
votes
4
replies
6.2k
views
TMM Normalization: DESeqDataSet: some values in assay are negative
deseq2 deseq normalization
updated 6.5 years ago by ▴ 40 • written 6.5 years ago by • 0
1
vote
2
replies
1.3k
views
Filtering extraneous samples affects DESeq results. What is going on?
deseq deseq2
updated 6.5 years ago by 43k • written 6.5 years ago by • 0
0
votes
0
replies
1.4k
views
Including sva results in SeqGSEA with data with batch effect
limma deseq2 seqgsea sva deseq
6.5 years ago kentfung ▴ 20
0
votes
9
replies
3.0k
views
NOOB question: How to use contrasts for subgroup analysis in DESeq2?
deseq deseq2 contrast subgroup
6.9 years ago ariel ▴ 20
3
votes
12
replies
2.5k
views
Why did I get NA p-values in DESeq with continuous variable?
deseq2 p-value continuous deseq
6.9 years ago ariel ▴ 20
2
votes
3
replies
2.7k
views
DESeq2 count outlier replacement from Cook's threshold
deseq2 deseq rnaseq outliers count outliers
updated 7.1 years ago by 43k • written 7.1 years ago by ▴ 10
0
votes
1
reply
1.5k
views
Question about multi-factor Deseq analysis
DESeq deseq2 microbiome gut microbiome
updated 7.2 years ago by 43k • written 7.2 years ago by • 0
0
votes
3
replies
1.7k
views
Strange lfcShrink plot when running DESeq2 workflow
DESeq2 rnaseq rna-seq deseq2 deseq
7.3 years ago Ben ▴ 50
0
votes
7
replies
4.5k
views
DESeq2 install problem
deseq
updated 7.3 years ago by 43k • written 7.3 years ago by • 0
512 results • Page 1 of 11
Recent ...
Replies
Comment: DESeq2 - how many surrogate variables from svaseq, use of lfcshrink by ja569116 • 0
Hi @atpoint Thanks for the information. Could you please expand on when to use adjusted p-values vs nominal p-values. My understanding was …
Answer: limpa analysis advice by Gordon Smyth 53k
It is actually very hard to estimate the DPC from observed data, because the curve is function of unobserved intensities rather than a func…
Answer: When to use edgeR or limma by Gordon Smyth 53k
The short answer is that we generally prefer edgeR for applications with lots of small counts and limma for complex designs with random eff…
Comment: limpa-blank normalization and Spectronaut's PTM stoichiometry by Gordon Smyth 53k
I updated the above answer today.
Answer: When to use edgeR or limma by James W. MacDonald 68k
I would use edgeR's quasi-likelihood model for any analysis with a smaller number of observations (like 3 vs 3 or similar), but if you have…
Votes
Answer: When to use edgeR or limma
Answer: When to use edgeR or limma
Answer: When to use edgeR or limma
Answer: When to use edgeR or limma
A: deseq2 - paired samples in 2 sequencing types with very different library sizes
Awards • All
Popular Question to Lluís Revilla Sancho ▴ 760
Popular Question to nromerov • 0
Popular Question to Thomas Girke ★ 1.7k
Teacher to Gordon Smyth 53k
Popular Question to Stephanie M. Gogarten ▴ 890
Locations • All
The city by the bay, 5 minutes ago
Barcelona, Spain, 54 minutes ago
The Netherlands, 1 hour ago
United States, 1 hour ago
European Union, 3 hours ago
Traffic: 884 users visited in the last hour
Content Search
Users
Tags
Badges
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6