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Dispersion
•
reset
4
votes
5
replies
1.2k
views
No counts, just fold change data
EdgeR
Estimation
Dispersion
2.9 years ago
Manal
• 0
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
3
votes
2
replies
4.0k
views
DESeq2 with high dispersions
deseq2
dispersion
low counts
8.8 years ago • updated 8.7 years ago
meeta.mistry
▴ 30
5
votes
7
replies
6.7k
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
0
votes
11
replies
2.2k
views
Strange dispersion plot
deseq2
dispersion
6.2 years ago
Moose123
• 0
3
votes
3
replies
1.8k
views
Differential Expression Analysis in edgeR using Anova
edger
anova
gene expression
Dispersion
updated 4.8 years ago by
onlychainsaw2019
• 0 • written 5.3 years ago by
ilovesuperheroes1993
• 0
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
0
votes
3
replies
725
views
Dispersion outliers genes
Dispersion
DESeq2
11 months ago
raya.fai
▴ 60
0
votes
13
replies
5.5k
views
DESeq2: Poor dispersion fit, even when a local or custom fit is used
deseq2
dispersion
6.0 years ago
Frederik Ziebell
▴ 20
8
votes
12
replies
8.7k
views
EdgeR: Explaning dispersion types to newbies
edger
dispersion
estimatedispersions
visualization
teaching
updated 5.8 years ago by
Aaron Lun
★ 28k • written 5.8 years ago by
Mr.RB
▴ 20
3
votes
3
replies
1.2k
views
DESseq2: Why can the dispersion be generelized over the conditions?
deseq2
dispersion
estimatedispersions
updated 5.8 years ago by
Ryan C. Thompson
★ 7.9k • written 5.8 years ago by
Mr.RB
▴ 20
1
vote
1
reply
890
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
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
0
votes
5
replies
2.5k
views
Dispersion calculation by DESeq2
DESeq2
dispersion
5.2 years ago
eva-m.petit
• 0
0
votes
6
replies
1.6k
views
DEXSeq dispersion outlier
DEXSeq
dispersion
pvalue
5.0 years ago
fiona.dick91
▴ 60
0
votes
2
replies
807
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
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
1
vote
2
replies
1.2k
views
Design formula in DESeq2
groups
dispersion
DESeq2
desing
2.4 years ago
m.glymenaki
• 0
0
votes
1
reply
1.2k
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
2
votes
2
replies
583
views
DESeq2 median of ratios normalization instead of VST or rlog for ordinations?
DESeq2
medianofratiostransformation
StatisticalMethod
Normalization
dispersion
3 months ago
Linton
• 0
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
4
votes
3
replies
1.6k
views
How to get dispersion values for DESeq2
deseq2
dispersion
R
updated 7.8 years ago by
Michael Love
41k • written 7.8 years ago by
hiraksarkar.cs
▴ 10
0
votes
0
replies
551
views
Range value of the dispersion parameters (a1, alpha 0 and sigmad)
polyester
dispersion
updated 3.0 years ago by
Michael Love
41k • written 3.0 years ago by
catalina.gonzalez-gomez
• 0
23 results • Page
1 of 1
Recent ...
Replies
Answer: DESEQ2 IHW and Apelgm method for Shrinkage (adding s values to FDR)
by
Michael Love
41k
> I got many p values that had "1.000000e+00" and padj "1" and stat of "0" when I added the Log threshold of LFC >1 and LFC < -1...is this …
Comment: Trying to use enrichGO
by
fernanda.backsouza
▴ 10
With all my love, thank you Guido, GOxploreR beeing a big ally for me. I don't know how to be grateful right now.
Comment: DESeq2 output used for PCA plot on R studio
by
swbarnes2
★ 1.3k
You didn't generate it with an experiment, you made it up: Your PCA doesn't look like a good RNASeq experiment, because it's not.
Answer: Opposite sign of LFC in count plots of DEGs (DESeq2)
by
swbarnes2
★ 1.3k
Your contrast is comparing LGR5 to Homeostasis. The bottom 2 are fine, it's the top one that is wrong. Are you sure this step isn't misla…
Comment: get BM error
by
James W. MacDonald
65k
I believe you need NCBI Gene IDs for KEGG, in which case you may need to map. The three genes you have shown here don't map, and of those t…
Votes
C: when to apply quantile normalization with voom in limma/voom framework with RNA-
A: How to know if I should use voomWithQualityWeights() or not?
A: Weird results (ribosomal proteins / Y-linked genes) in limma/voom
Answer: Log-cpm values from limma
Answer: Log-cpm values from limma
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