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lfcShrink
•
reset
0
votes
4
replies
769
views
Should I use the 'log2FoldChange' from lfcShrink() to subset significant DEGs?
lfcshrink
DESeq2
written 5 months ago by
Igor
• 0
0
votes
2
replies
645
views
DESeq2 : stat or lfcshrink for GSEA analysis
lfcshrink
GSEABenchmarkeR
DESeq2
updated 6 months ago by
ATpoint
★ 4.2k • written 6 months ago by
delphine.rossille
• 0
3
votes
4
replies
932
views
lfcShrink() and batch effects in DESeq2
BatchEffect
lfcshrink
RNA-seq
DESeq2
10 months ago
Eva
▴ 10
1
vote
1
reply
2.5k
views
Question regarding lfcShrink types in DiffBind
FoldChange
DiffBind
lfcShrink
updated 10 months ago by
Rory Stark
★ 5.2k • written 11 months ago by
bhandary.8590
▴ 20
4
votes
4
replies
900
views
DESeq2 lfcShrink function used in DiffBind package
FoldChange
DiffBind
lfcShrink
Cut&TagData
12 months ago • updated 11 months ago
bhandary.8590
▴ 20
2
votes
17
replies
1.9k
views
lfcshrink error DESeq2
DESeq2
lfcshrink
DESe
updated 13 months ago by
Michael Love
42k • written 13 months ago by
Alina
• 0
1
vote
1
reply
851
views
Identifying DEGs using lfcshrink()
DESeq2
lfcshrink
updated 20 months ago by
Michael Love
42k • written 20 months ago by
Zainab
▴ 10
1
vote
3
replies
1.1k
views
resultsNames(dds) not showing all contrasts
DESeq2
resultsNames
lfcShrink
updated 21 months ago by
ATpoint
★ 4.2k • written 21 months ago by
eve.olszanowski
• 0
1
vote
2
replies
1.8k
views
DEseq2 anlysis - LfcThreshold and Lfcshrink options
lfcshrink
DESeq2
RNASeq
lfcthreshold
23 months ago
ClaudiaE
• 0
2
votes
4
replies
2.5k
views
ashr vs apeglm for interaction data
lfcShrink
DESeq2
2.1 years ago
Ali Barry
▴ 40
1
vote
3
replies
934
views
Why are padj results different for BetaPrior = TRUE vs lfcShrink()?
IHW
lfcShrink
DESeq2
2.2 years ago
Ali Barry
▴ 40
0
votes
3
replies
982
views
lfcShrink contrast
lfcshrink
R
DESeq2
updated 2.2 years ago by
ATpoint
★ 4.2k • written 2.2 years ago by
LHA_trash
• 0
4
votes
1
reply
1.1k
views
DEGs from lfcshrink() and results()
lfcshrink
DESeq2
updated 2.4 years ago by
ATpoint
★ 4.2k • written 2.4 years ago by
BT
▴ 10
1
vote
3
replies
1.4k
views
Correct use of Likelihood Ratio Test and LFC Shrinkage
RNASeq
LRT
DESeq2
lfcShrink
updated 16 months ago by
ayabalbaa1990
• 0 • written 2.4 years ago by
Emma
• 0
0
votes
1
reply
764
views
Variation in number of DEGs on LFC shrinkage
DESeq2
lfcShrink
updated 2.6 years ago by
Michael Love
42k • written 2.6 years ago by
Deevanshu
• 0
0
votes
1
reply
734
views
lfcshrink() and 2 conditions, 3 genotypes
lfcshrink
DESeq2
updated 2.6 years ago by
Michael Love
42k • written 2.6 years ago by
Nayrouz
• 0
2
votes
2
replies
933
views
Negative svalues from DESeq2 lfcShrink with ashr
ashr
DESeq2
lfcShrink
svalue
3.3 years ago
Enrico
• 0
2
votes
5
replies
2.9k
views
Error in lfcShrink
lfcShrink
DESeq2
updated 3.6 years ago by
tcalvo
▴ 90 • written 3.6 years ago by
Claudio Carril
• 0
2
votes
3
replies
2.0k
views
lfcshrink() with no coef in resultsNames()
lfcshrink
coef
DESeq2
updated 2.6 years ago by
Michael Love
42k • written 3.6 years ago by
Assa Yeroslaviz
★ 1.5k
1
vote
1
reply
802
views
LFCshrink function understanding
deseq2
MAplot
lfcshrink
updated 3.8 years ago by
Michael Love
42k • written 3.8 years ago by
evelas13
• 0
1
vote
1
reply
21k
views
Why does the DESEQ2 lfcshrink function results not include the stat variable
deseq2
stat
lfcshrink
4.2 years ago
divercory
• 0
1
vote
1
reply
25k
views
lfcShrink doesn't work with contrasts
lfcShrink
contrast
design
deseq2
updated 4.4 years ago by
Michael Love
42k • written 4.4 years ago by
Assa Yeroslaviz
★ 1.5k
0
votes
2
replies
969
views
Coefficient names for multiple group comparisons to use with lfcShrink & apeglm
deseq2
lfcShrink
apeglm
updated 4.5 years ago by
Michael Love
42k • written 4.5 years ago by
coulsonr
▴ 20
22
votes
17
replies
7.4k
views
DESeq2 1.20.0 lfcshrink function
deseq2
differential expression
logfoldchange
lfcshrink
lfcthreshold
updated 3.1 years ago by
Michael Love
42k • written 6.0 years ago by
emi.sch
▴ 30
0
votes
1
reply
873
views
DESeq2: three conditions lfcShrink CvsB analysis
deseq2
lfcShrink
updated 5.0 years ago by
Michael Love
42k • written 5.0 years ago by
kcbauer
• 0
3
votes
3
replies
1.1k
views
lfc shrinkage two factor experiment
deseq2
lfcShrink
updated 5.1 years ago by
Michael Love
42k • written 5.1 years ago by
rbutler
• 0
1
vote
6
replies
1.6k
views
Zero pvalues after lfcShrink of DESeq2 package
deseq2
pvalue
lfcshrink
updated 5.2 years ago by
Michael Love
42k • written 5.2 years ago by
peibo_xu
▴ 10
0
votes
4
replies
1.9k
views
DESeq2 lfcShrink with interactions
deseq2
lfcShrink
interactions
updated 5.4 years ago by
Michael Love
42k • written 5.4 years ago by
hannepainter
• 0
3
votes
5
replies
1.5k
views
lfcShrink, interactions, and ashr
deseq2
lfcshrink
contrast
updated 5.5 years ago by
Michael Love
42k • written 5.5 years ago by
jurbach
▴ 10
0
votes
1
reply
1.1k
views
DESeq2 - shrunken log fold changes and threshold test
deseq2
lfcshrink
lfcthreshold
differential gene expression
updated 5.6 years ago by
Michael Love
42k • written 5.6 years ago by
corentinrichard374369
• 0
4
votes
2
replies
2.6k
views
Interpreting the results from lfcShrink() with apeglm in DESeq2
deseq2
apeglm
lfcshrink
updated 5.7 years ago by
Michael Love
42k • written 5.7 years ago by
charles.foster
▴ 160
0
votes
2
replies
1.1k
views
lfcshrink in DESeq2 with grouping variable
deseq2
lfcshrink
updated 5.8 years ago by
Michael Love
42k • written 5.8 years ago by
kendralec
▴ 10
1
vote
4
replies
1.7k
views
Log2 fold-change shrinkage fails with lfcShrink when using the 'apeglm' method
deseq2
apeglm
lfcshrink
5.9 years ago
coulsonr
▴ 20
5
votes
4
replies
2.1k
views
lfcShrink behavior with homogeneous expression dataset
deseq2
lfcshrink
betaprior
updated 5.9 years ago by
Michael Love
42k • written 5.9 years ago by
mat.lesche
▴ 90
10
votes
6
replies
5.5k
views
Log2FoldChange shrinkage method in DESeq2
deseq2
apeglm
lfcshrink
updated 6.1 years ago by
Michael Love
42k • written 6.1 years ago by
Benjamin Ostendorf
▴ 90
0
votes
1
reply
1.3k
views
DESeq2::lfcshrink() for complex contrast designs
deseq2
lfcshrink
interaction term
updated 6.1 years ago by
Michael Love
42k • written 6.1 years ago by
krutherford
• 0
2
votes
4
replies
1.9k
views
DESeq2 with multi level
deseq2
lfcshrink
updated 6.1 years ago by
Michael Love
42k • written 6.2 years ago by
pierre.k
• 0
0
votes
3
replies
5.6k
views
How are the shrunk result data used in DESeq2?
deseq2
lfcshrink
updated 6.2 years ago by
Michael Love
42k • written 6.2 years ago by
thkapell
▴ 10
1
vote
2
replies
940
views
DESeq2 lfcShrink time for analysis
deseq2
lfcshrink
updated 6.3 years ago by
ellascottgm
• 0 • written 6.4 years ago by
jshouse
▴ 10
1
vote
12
replies
4.0k
views
DESeq2 LFC shrinkage is for designs with interactions
deseq2
lfcshrink
6.4 years ago
yk.gatc
• 0
3
votes
19
replies
5.8k
views
lfcShrink and factors with multiple levels
deseq2
lfcshrink
relevel
updated 6.6 years ago by
Michael Love
42k • written 6.6 years ago by
mat.lesche
▴ 90
1
vote
1
reply
1.2k
views
DESeq2 parallel argument for lfcShrink
deseq2
lfcshrink
updated 6.6 years ago by
Michael Love
42k • written 6.7 years ago by
dsull
• 0
0
votes
9
replies
1.9k
views
lfcshrink and rlog take forever to compute with a DESeqDataSet with many genotypes and conditions
deseq2
lfcshrink
rlog
6.8 years ago
pecot
• 0
1
vote
2
replies
1.5k
views
DESeq2 version 1.16.1 installation and difference with version 1.14.1
deseq2
betaprior=true
lfcshrink
updated 6.8 years ago by
James W. MacDonald
66k • written 6.8 years ago by
tarun2
• 0
1
vote
4
replies
2.2k
views
Error when using lfcShrink and contrast argument in DESeq2
deseq2
lfcshrink
6.8 years ago
Oskar
▴ 50
0
votes
1
reply
1.3k
views
lfcShrink-coef option. Desired coefficient not appearing.
deseq2
lfcShrink
updated 6.9 years ago by
Michael Love
42k • written 6.9 years ago by
Victor Barrera
• 0
46 results • Page
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Comment: gds in GEOmetadb 2023-06-26 version is empty
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Frederico Moraes Ferreira
▴ 100
Try axel -n 20 https://gbnci.cancer.gov/geo/GEOmetadb.sqlite.gz
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The default for `enrichGO` is to subset to those with a p-value<0.05. You don't adjust that default argument, so you shouldn't have any GO …
Answer: In a 3 group DEG analysis with three batches, can I use 1 group in all three bat
by
Michael Love
42k
You can compare A and C thanks to the sharing of samples from B across 1, 2 and 3.
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by
adripel
• 0
In the enrichGO results we have significant and non-significant enriched terms that are displayed. So why would an enriched term (significa…
Answer: Design formula, numeric contrast, and lfcshrink in deseq2
by
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42k
For questions about how to construct the correct contrasts correspond to particular hypotheses, I recommend consulting with a local statist…
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