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Showing :
dispersion
•
reset
2
votes
2
replies
634
views
DESeq2 median of ratios normalization instead of VST or rlog for ordinations?
DESeq2
medianofratiostransformation
StatisticalMethod
Normalization
dispersion
4 months ago • updated 3 months ago
Linton
• 0
0
votes
3
replies
742
views
Dispersion outliers genes
Dispersion
DESeq2
11 months ago
raya.fai
▴ 60
1
vote
1
reply
901
views
Dispersion estimates with DESeq2
dispersionestimates
dispersion
DESeq2
estimates
deseq2
updated 21 months ago by
Michael Love
41k • written 21 months ago by
Julia
▴ 10
1
vote
2
replies
1.2k
views
Design formula in DESeq2
groups
dispersion
DESeq2
desing
2.4 years ago
m.glymenaki
• 0
4
votes
5
replies
1.2k
views
No counts, just fold change data
EdgeR
Estimation
Dispersion
2.9 years ago
Manal
• 0
0
votes
0
replies
554
views
Range value of the dispersion parameters (a1, alpha 0 and sigmad)
polyester
dispersion
updated 3.1 years ago by
Michael Love
41k • written 3.1 years ago by
catalina.gonzalez-gomez
• 0
3
votes
6
replies
2.9k
views
DESeq2: When to split multiple group samples for 'more' accurate sizefactors, dispersions etc.
Dispersion
RNA-seq
DESeq2
Multiple-group
updated 3.2 years ago by
Michael Love
41k • written 3.5 years ago by
Kelen
▴ 10
0
votes
2
replies
816
views
Normalization and dispersion estimates in timeseries data with highly variable read numbers
EdgeR
dispersion
normalization
updated 4.2 years ago by
Gordon Smyth
50k • written 4.2 years ago by
Ruben.wauters
• 0
0
votes
6
replies
1.6k
views
DEXSeq dispersion outlier
DEXSeq
dispersion
pvalue
5.0 years ago
fiona.dick91
▴ 60
0
votes
5
replies
2.5k
views
Dispersion calculation by DESeq2
DESeq2
dispersion
5.3 years ago
eva-m.petit
• 0
0
votes
4
replies
1.4k
views
DESeq2 for analyzing differential expression based on dispersion across samples within groups, instead of based on expression means.
deseq2
dispersion
updated 5.3 years ago by
Michael Love
41k • written 5.3 years ago by
emilio.marmol
• 0
3
votes
3
replies
1.8k
views
Differential Expression Analysis in edgeR using Anova
edger
anova
gene expression
Dispersion
updated 4.9 years ago by
onlychainsaw2019
• 0 • written 5.3 years ago by
ilovesuperheroes1993
• 0
3
votes
3
replies
1.2k
views
DESseq2: Why can the dispersion be generelized over the conditions?
deseq2
dispersion
estimatedispersions
updated 5.9 years ago by
Ryan C. Thompson
★ 7.9k • written 5.9 years ago by
Mr.RB
▴ 20
8
votes
12
replies
8.8k
views
EdgeR: Explaning dispersion types to newbies
edger
dispersion
estimatedispersions
visualization
teaching
updated 5.9 years ago by
Aaron Lun
★ 28k • written 5.9 years ago by
Mr.RB
▴ 20
0
votes
13
replies
5.5k
views
DESeq2: Poor dispersion fit, even when a local or custom fit is used
deseq2
dispersion
6.1 years ago
Frederik Ziebell
▴ 20
0
votes
11
replies
2.2k
views
Strange dispersion plot
deseq2
dispersion
6.2 years ago
Moose123
• 0
5
votes
7
replies
6.8k
views
DESeq2 dispersion and p-value histograms
deseq2
rnaseq
fdrtool
dispersion
updated 6.5 years ago by
Bernd Klaus
▴ 610 • written 6.5 years ago by
rrcutler
▴ 70
1
vote
2
replies
1.0k
views
2-Factor Experiment in edgeR, Effect of no reps in one set and two reps in others
rnaseq
edger
differential expression
dispersion
updated 7.5 years ago by
Ryan C. Thompson
★ 7.9k • written 7.5 years ago by
nancyjwahl7
• 0
4
votes
3
replies
1.6k
views
How to get dispersion values for DESeq2
deseq2
dispersion
R
updated 7.9 years ago by
Michael Love
41k • written 7.9 years ago by
hiraksarkar.cs
▴ 10
1
vote
2
replies
1.4k
views
Common dispersion from estimateGLMRobustDisp()
edgeR
dispersion
updated 7.9 years ago by
Aaron Lun
★ 28k • written 7.9 years ago by
Jane Merlevede
▴ 90
1
vote
3
replies
2.1k
views
Error Estimating the NB Dispersion of a Dataset
dispersion
edgeR
updated 7.9 years ago by
Gordon Smyth
50k • written 7.9 years ago by
humberto_munoz
• 0
0
votes
1
reply
1.3k
views
How do I turn off dispersion in DESeq2?
deseq2
dispersion
updated 8.2 years ago by
Michael Love
41k • written 8.2 years ago by
hans
• 0
3
votes
2
replies
4.0k
views
DESeq2 with high dispersions
deseq2
dispersion
low counts
8.8 years ago
meeta.mistry
▴ 30
23 results • Page
1 of 1
Recent ...
Replies
Comment: Too many significant genes when integrating gtex and tcga
by
ATpoint
★ 4.1k
These two datasets are from completely different experiments / batches. It is utterly meaningless to compare them. I would suggest comparat…
Answer: fgsea significant result
by
ATpoint
★ 4.1k
Set a fixed seed before running this. Note that a FDR of 0.25 in fgsea is wildly and overly lenient. See https://support.bioconductor.o…
Answer: How to use bootRanges to bootstrap small RNA loci (nullranges package)
by
Poonam
• 0
Hi Michael, I think there is something wrong with the generation of nullranges. I was working with small RNA and methylation overlaps. …
Answer: Once again a "Model matrix not full rank"
by
swbarnes2
★ 1.3k
Replicate numbers, like the 1 in control_1 are fine in sample names, but never add them to anything else in colData. From the computer's p…
Answer: limma Intercept vs No-intercept models completely changing DMR results?
by
Gordon Smyth
50k
I'll add a little bit of general advice to James' answer. You seem to have the misunderstanding that you can change the design matrix but …
Votes
Answer: Why does GSEA on edgeR results for randomized samples give highly significant p-
Answer: limma Intercept vs No-intercept models completely changing DMR results?
Answer: CombineArrays for EPIC and EPIC V2
Answer: Too many significant genes when integrating gtex and tcga
Comment: Too many significant genes when integrating gtex and tcga
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