Showing : DEseq • reset
40
votes
44
replies
7.3k
views
Are published RNA seq data analyses often wrong in calculating p-values and FDR?
FDR p-value DESeq RNA-Seq
updated 4.4 years ago by ▴ 60 • written 5.0 years ago by ▴ 10
25
votes
11
replies
6.2k
views
Normalization methodology in DESeq/DESeq2 vs edgeR
deseq deseq2 edgeR normalization
updated 6.5 years ago by ★ 3.7k • written 6.5 years ago by ▴ 70
24
votes
22
replies
13k
views
DESeq2 for ChIP-seq differential peaks
deseq2 deseq chipseq
updated 4.9 years ago by ▴ 100 • written 6.7 years ago by ▴ 190
15
votes
5
replies
5.8k
views
DESeq and Limma+Voom Normalization for Rna-Seq Data Using Ercc Spike-In
limma voom deseq normalization ercc
updated 6.5 years ago by 45k • written 6.5 years ago by ▴ 100
15
votes
8
replies
9.7k
views
DESeq2 - Acquiring batch-corrected values for PCA and hierarchical clustering
deseq2 deseq
7.5 years ago salahm ▴ 70
14
votes
15
replies
39k
views
DESeq2 output explanation
deseq deseq2
updated 6 months ago by 36k • written 7.5 years ago by ▴ 80
11
votes
9
replies
10k
views
How does DESeq2 handle zero counts in one condition?
deseq2 deseq rna-seq
7.4 years ago gavrielmatt ▴ 10
10
votes
14
replies
9.4k
views
how DESeq calculates p-value ?
deseq differential gene expression statistics p-value
updated 14 months ago by ▴ 20 • written 6.3 years ago by ▴ 30
10
votes
14
replies
2.5k
views
Why limma, edgeR, and DESeq did not implement fold change moderation first?
limma edger deseq deseq2
updated 4.7 years ago by 45k • written 4.7 years ago by ▴ 70
9
votes
6
replies
5.5k
views
DESeq2 multiple interaction terms 3-factor design
deseq2 deseq interactions multiple factor design
updated 6.4 years ago by 36k • written 6.4 years ago by ▴ 270
9
votes
17
replies
888
views
DESeq2 design subcategories
deseq2 deseq differential binding analysis
updated 4.4 years ago by 36k • written 4.4 years ago by ▴ 60
9
votes
6
replies
6.2k
views
Error bars DESeq or DESeq2 fold change
rnaseq deseq2 deseq standard error confidence interval
updated 6 months ago by 36k • written 6.1 years ago by ▴ 10
8
votes
4
replies
1.4k
views
DESeq2: interaction term as in limma
deseq2 deseq limma interaction term
updated 5.1 years ago by ★ 3.7k • written 5.1 years ago by ▴ 70
8
votes
2
replies
1.9k
views
Statistical analysis of Spectral count data : edgeR, limma or others ?
spectral counts proteomics limma edger deseq
updated 6.9 years ago by 45k • written 6.9 years ago by ▴ 60
7
votes
3
replies
2.9k
views
DESeq2 with interaction using SVA
deseq2 sva interaction term grouping variable deseq
4.3 years ago kevin.kingsland ▴ 60
7
votes
12
replies
7.9k
views
Confused in the usage of formula in DESeq or DESeq2
deseq2 deseq
updated 5.0 years ago by ▴ 60 • written 7.6 years ago by ▴ 20
6
votes
12
replies
10k
views
Problem making DESeq dataset; Error all variables in design formula must be columns in colData
deseq2 deseq counts rnaseq differential gene expression
updated 6.1 years ago by 36k • written 6.1 years ago by ▴ 10
6
votes
7
replies
2.8k
views
RUVseq PCA on raw data, whereas DESeq suggests stabilization
ruvseq deseq
6.5 years ago tonja.r ▴ 60
5
votes
2
replies
967
views
Is the VST implemented in DESeq useful on time-series cell differentiation datasets?
deseq deseq2 vst
updated 5.1 years ago by 13k • written 5.1 years ago by • 0
5
votes
3
replies
6.0k
views
What problem does the MA plot diagnose? And how do you solve it?
deseq2 deseq rnaseq
updated 5.2 years ago by 7.8k • written 5.2 years ago by ▴ 40
5
votes
18
replies
6.1k
views
Differential expression analysis: Continuous variables
DESeq EdgeR limma
6.7 years ago • updated 6.6 years ago Radek ▴ 90
5
votes
13
replies
3.7k
views
P values from Deseq Analysis
deseq
5.0 years ago Shrikant Pawar • 0
4
votes
7
replies
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
4
votes
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
4
votes
4
replies
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
4
votes
6
replies
793
views
DESeq2 design and stats question
deseq2 differential binding analysis deseq atac-seq
updated 4.3 years ago by 36k • written 4.3 years ago by ▴ 60
4
votes
3
replies
2.3k
views
Add new columns to DESeqResults from text file by matching rownames.
deseq2 deseq merge data frames cbind s4vectors
updated 4.6 years ago by 36k • written 4.6 years ago by • 0
4
votes
7
replies
758
views
Filtering DESeq2 result export along multiple lines
deseq2 differential binding analysis deseq
updated 4.5 years ago by 36k • written 4.5 years ago by ▴ 60
4
votes
3
replies
2.2k
views
Why does Deseq, Deseq2, and EdgeR give vastly different results.
edger deseq deseq2
4.9 years ago michael.steffen ▴ 20
4
votes
2
replies
7.0k
views
Analyzing RNA-Seq data without replicates using DESeq
deseq DESeq2
updated 7.7 years ago by 36k • written 7.7 years ago by ▴ 70
4
votes
14
replies
9.9k
views
standard error value (lfcSE) returned by DeSeq2
deseq2 deseq lfc lfcse standard error
updated 5.1 years ago by • 0 • written 5.2 years ago by • 0
4
votes
11
replies
21k
views
With DESeq2 "Not full rank" Error with design ~ line + time + condition
deseq deseq2
updated 7.3 years ago by 36k • written 7.3 years ago by ▴ 20
4
votes
6
replies
511
views
Interpretation of DESeq2 results with 3 factorial design with interaction terms.
r DESeq DESeq2
7 months ago s-rhussien • 0
3
votes
4
replies
2.5k
views
Variance filtering prior to RNA-seq differential expression
sequencing deseq limma
updated 6.8 years ago by 45k • written 6.8 years ago by ▴ 400
3
votes
12
replies
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
3
votes
5
replies
3.5k
views
Labeling points with hgnc symbols on the MA plot in DESeq2
deseq MA
updated 5.8 years ago by ▴ 150 • written 5.8 years ago by • 0
3
votes
3
replies
1.3k
views
read counts of paired end reads for DESeq2 analysis
deseq featurecounts paired
updated 6.1 years ago by 13k • written 6.1 years ago by • 0
3
votes
5
replies
4.8k
views
DESeq2 resultsNames output
deseq deseq2
updated 7.3 years ago by 36k • written 7.3 years ago by ▴ 40
3
votes
14
replies
16k
views
Normalization in DESeq2
deseq2 deseq
updated 7.4 years ago by 36k • written 7.4 years ago by ▴ 70
3
votes
7
replies
594
views
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
3
votes
5
replies
536
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 2.1 years ago by 36k • written 2.1 years ago by ▴ 780
3
votes
11
replies
2.3k
views
DESeq function taking too long
deseq2 deseq factor rnaseq
updated 4.8 years ago by ★ 2.6k • written 4.8 years ago by ▴ 30
3
votes
4
replies
2.6k
views
DESeq is better than DESeq2?
deseq2 deseq
6.1 years ago ribioinfo ▴ 100
3
votes
8
replies
3.2k
views
DESeq / DESeq2 for translation efficiency in polysome profiling or ribsome profiling experiments
Sequencing DESeq Sequencing DESeq
updated 5.7 years ago by • 0 • written 8.4 years ago by ★ 12k
3
votes
1
reply
878
views
RNASeq testing for differential expression in one condition, equality in another (using DESeq)
deseq2 deseq rnaseq
5.2 years ago ysdel ▴ 40
3
votes
5
replies
2.3k
views
Using DESeq2: experimental design and extracting results
DESeq DESeq2 DESeq DESeq2
updated 8.0 years ago by 36k • written 8.0 years ago by ▴ 60
3
votes
5
replies
1.7k
views
DESeq on transcripts v/s genes
DESeq DESeq
updated 10.3 years ago by 13k • written 10.3 years ago by ▴ 410
3
votes
2
replies
2.4k
views
Nanostring ncounterdata - DESeq
RNASeq Normalization Preprocessing DESeq RNASeq Normalization Preprocessing DESeq
updated 10.8 years ago by ★ 3.7k • written 10.8 years ago by ▴ 20
3
votes
5
replies
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
3
votes
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
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
Awards • All
Scholar to Gordon Smyth 45k
Popular Question to andrebolerbarros ▴ 10
Scholar to James W. MacDonald 59k
Scholar to Guido Hooiveld ★ 3.2k
Scholar to Kevin Blighe 3.5k
Locations • All
V&A Waterfront, Cape Town, South Africa, 7 minutes ago
Germany, 8 minutes ago
India, 36 minutes ago
Switzerland, 1 hour ago
Portugal, 1 hour ago
Traffic: 335 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