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Deseq2
•
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2
votes
6
replies
81
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Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
DESeq2
RUVSeq
RUVseq
BatchEffect
DES
updated 30 minutes ago by
SamGG
▴ 350 • written 5 hours ago by
Alexandre
• 0
0
votes
1
reply
45
views
PCA plot suggestions
DESeq2
PCAtools
updated 3 hours ago by
JKim
• 0 • written 14 hours ago by
Aaliya
• 0
0
votes
1
reply
73
views
DESEQ2 IHW and Apelgm method for Shrinkage (adding s values to FDR)
DESeq2
RNAseq
updated 21 hours ago by
Michael Love
41k • written 1 day ago by
kcarey
• 0
1
vote
3
replies
90
views
Different Shrunk Log2FC according with reference
DESeq2
updated 1 day ago by
Michael Love
41k • written 1 day ago by
andrebolerbarros
▴ 20
0
votes
3
replies
109
views
Opposite sign of LFC in count plots of DEGs (DESeq2)
DESeq2
updated 4 hours ago by
James W. MacDonald
65k • written 1 day ago by
winwater0928
• 0
3
votes
1
reply
197
views
Use of negative binomial model for exponential decay rate estimation using DESeq (or similar)
DESeq2
updated 1 day ago by
Michael Love
41k • written 1 day ago by
i.sudbery
▴ 40
0
votes
8
replies
228
views
DESeq2 output used for PCA plot on R studio
DESeq2
RSTUDIO
PCAtools
updated 12 hours ago by
swbarnes2
★ 1.3k • written 2 days ago by
Aaliya
• 0
3
votes
3
replies
157
views
DESeq2 - dispersion estimation when there is none
DESeq2
updated 2 days ago by
Michael Love
41k • written 3 days ago by
WardDeb
• 0
0
votes
4
replies
195
views
Differential peaks that were not identified in diffbind were identified in diseq2
DiffBind
DESeq2
ATACSeq
8 days ago • updated 5 days ago
lonn
• 0
1
vote
2
replies
220
views
How to retrieve detailed regression results from deseq2
DESeq2
14 days ago • updated 5 days ago
Weiqian
▴ 10
0
votes
4
replies
229
views
DEG with low counts
DESeq2
updated 6 days ago by
Michael Love
41k • written 10 days ago by
Rajat
• 0
0
votes
7
replies
387
views
DESeq filtering specific to contrasts
DESeq2
updated 6 days ago by
Michael Love
41k • written 9 weeks ago by
Emma
• 0
6
votes
16
replies
2.3k
views
DESeq2 a lot of genes showing up as differentially expressed that only have 1 sample with any expression
deseq2
updated 2 days ago by
Michael Love
41k • written 4.6 years ago by
hsbio
▴ 10
2
votes
5
replies
698
views
DESeq2 setting significant p-value
DESeq2
updated 6 days ago by
Michael Love
41k • written 5.0 years ago by
Merlin
▴ 10
14 results • Page
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Replies
Comment: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
by
SamGG
▴ 350
Is useless the assumption that the majority of genes have no variation in expression (bearing in mind that they are distributed over the en…
Comment: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
by
Alexandre
• 0
Hello James, Thank you for your answer and precise exemple ! It is disappointing but makes sense. Best, Alexandre
Comment: How to retrieve gene ontology GO class from gene list?
by
James W. MacDonald
65k
Yes. The `keys` argument to both `select` and `mapIds` will accept a vector (see `?select` for more information). Also, the [vignette][1] f…
Comment: How to retrieve gene ontology GO class from gene list?
by
bandconductor
• 0
Thanks, this is potentially a much faster way than parsing BiomRt. However, it is only returning one GO term right now (biomaRt returns a f…
Comment: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
by
James W. MacDonald
65k
Both `RUVseq` and `sva` are meant to be used to remove technical variability. The problem is the identification of variability that is tech…
Votes
Answer: Cross-species analysis - how to compute the mid parent value?
Answer: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
Answer: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
Answer: Use of negative binomial model for exponential decay rate estimation using DESeq
C: null model and DEXSeqDataSet object in DEXSEQ
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