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lfcshrink
•
reset
0
votes
4
replies
655
views
Should I use the 'log2FoldChange' from lfcShrink() to subset significant DEGs?
lfcshrink
DESeq2
written 4 months ago by
Igor
• 0
0
votes
2
replies
504
views
DESeq2 : stat or lfcshrink for GSEA analysis
lfcshrink
GSEABenchmarkeR
DESeq2
updated 4 months ago by
ATpoint
★ 4.0k • written 4 months ago by
delphine.rossille
• 0
3
votes
4
replies
847
views
lfcShrink() and batch effects in DESeq2
BatchEffect
lfcshrink
RNA-seq
DESeq2
8 months ago
Eva
▴ 10
1
vote
1
reply
2.2k
views
Question regarding lfcShrink types in DiffBind
FoldChange
DiffBind
lfcShrink
updated 9 months ago by
Rory Stark
★ 5.1k • written 9 months ago by
bhandary.8590
▴ 20
4
votes
4
replies
790
views
DESeq2 lfcShrink function used in DiffBind package
FoldChange
DiffBind
lfcShrink
Cut&TagData
10 months ago
bhandary.8590
▴ 20
2
votes
17
replies
1.7k
views
lfcshrink error DESeq2
DESeq2
lfcshrink
DESe
updated 11 months ago by
Michael Love
41k • written 11 months ago by
Alina
• 0
1
vote
1
reply
777
views
Identifying DEGs using lfcshrink()
DESeq2
lfcshrink
updated 18 months ago by
Michael Love
41k • written 18 months ago by
Zainab
• 0
1
vote
3
replies
986
views
resultsNames(dds) not showing all contrasts
DESeq2
resultsNames
lfcShrink
updated 20 months ago by
ATpoint
★ 4.0k • written 20 months ago by
eve.olszanowski
• 0
1
vote
2
replies
1.7k
views
DEseq2 anlysis - LfcThreshold and Lfcshrink options
lfcshrink
DESeq2
RNASeq
lfcthreshold
21 months ago
ClaudiaE
• 0
2
votes
4
replies
2.3k
views
ashr vs apeglm for interaction data
lfcShrink
DESeq2
23 months ago
Ali Barry
▴ 40
1
vote
3
replies
878
views
Why are padj results different for BetaPrior = TRUE vs lfcShrink()?
IHW
lfcShrink
DESeq2
2.0 years ago
Ali Barry
▴ 40
0
votes
3
replies
929
views
lfcShrink contrast
lfcshrink
R
DESeq2
updated 2.0 years ago by
ATpoint
★ 4.0k • written 2.0 years ago by
LHA_trash
• 0
4
votes
1
reply
1.1k
views
DEGs from lfcshrink() and results()
lfcshrink
DESeq2
updated 2.2 years ago by
ATpoint
★ 4.0k • written 2.2 years ago by
BT
▴ 10
1
vote
3
replies
1.3k
views
Correct use of Likelihood Ratio Test and LFC Shrinkage
RNASeq
LRT
DESeq2
lfcShrink
updated 14 months ago by
ayabalbaa1990
• 0 • written 2.2 years ago by
Emma
• 0
0
votes
1
reply
738
views
Variation in number of DEGs on LFC shrinkage
DESeq2
lfcShrink
updated 2.4 years ago by
Michael Love
41k • written 2.4 years ago by
Deevanshu
• 0
0
votes
1
reply
694
views
lfcshrink() and 2 conditions, 3 genotypes
lfcshrink
DESeq2
updated 2.5 years ago by
Michael Love
41k • written 2.5 years ago by
Nayrouz
• 0
2
votes
2
replies
888
views
Negative svalues from DESeq2 lfcShrink with ashr
ashr
DESeq2
lfcShrink
svalue
3.1 years ago
Enrico
• 0
2
votes
3
replies
1.9k
views
lfcshrink() with no coef in resultsNames()
lfcshrink
coef
DESeq2
updated 2.5 years ago by
Michael Love
41k • written 3.4 years ago by
Assa Yeroslaviz
★ 1.5k
2
votes
5
replies
2.8k
views
Error in lfcShrink
lfcShrink
DESeq2
updated 3.4 years ago by
tcalvo
▴ 90 • written 3.5 years ago by
Claudio Carril
• 0
1
vote
1
reply
770
views
LFCshrink function understanding
deseq2
MAplot
lfcshrink
updated 3.6 years ago by
Michael Love
41k • written 3.6 years ago by
evelas13
• 0
1
vote
1
reply
20k
views
Why does the DESEQ2 lfcshrink function results not include the stat variable
deseq2
stat
lfcshrink
4.1 years ago
divercory
• 0
1
vote
1
reply
25k
views
lfcShrink doesn't work with contrasts
lfcShrink
contrast
design
deseq2
updated 4.3 years ago by
Michael Love
41k • written 4.3 years ago by
Assa Yeroslaviz
★ 1.5k
0
votes
2
replies
929
views
Coefficient names for multiple group comparisons to use with lfcShrink & apeglm
deseq2
lfcShrink
apeglm
updated 4.3 years ago by
Michael Love
41k • written 4.3 years ago by
coulsonr
▴ 20
0
votes
1
reply
834
views
DESeq2: three conditions lfcShrink CvsB analysis
deseq2
lfcShrink
updated 4.8 years ago by
Michael Love
41k • written 4.8 years ago by
kcbauer
• 0
3
votes
3
replies
1.1k
views
lfc shrinkage two factor experiment
deseq2
lfcShrink
updated 5.0 years ago by
Michael Love
41k • written 5.0 years ago by
rbutler
• 0
1
vote
6
replies
1.5k
views
Zero pvalues after lfcShrink of DESeq2 package
deseq2
pvalue
lfcshrink
updated 5.1 years ago by
Michael Love
41k • written 5.1 years ago by
peibo_xu
▴ 10
0
votes
4
replies
1.9k
views
DESeq2 lfcShrink with interactions
deseq2
lfcShrink
interactions
updated 5.2 years ago by
Michael Love
41k • written 5.2 years ago by
hannepainter
• 0
3
votes
5
replies
1.5k
views
lfcShrink, interactions, and ashr
deseq2
lfcshrink
contrast
updated 5.4 years ago by
Michael Love
41k • written 5.4 years ago by
jurbach
▴ 10
0
votes
1
reply
1.0k
views
DESeq2 - shrunken log fold changes and threshold test
deseq2
lfcshrink
lfcthreshold
differential gene expression
updated 5.4 years ago by
Michael Love
41k • written 5.4 years ago by
corentinrichard374369
• 0
4
votes
2
replies
2.5k
views
Interpreting the results from lfcShrink() with apeglm in DESeq2
deseq2
apeglm
lfcshrink
updated 5.6 years ago by
Michael Love
41k • written 5.6 years ago by
charles.foster
▴ 160
0
votes
2
replies
1.1k
views
lfcshrink in DESeq2 with grouping variable
deseq2
lfcshrink
updated 5.7 years ago by
Michael Love
41k • written 5.7 years ago by
kendralec
▴ 10
1
vote
4
replies
1.6k
views
Log2 fold-change shrinkage fails with lfcShrink when using the 'apeglm' method
deseq2
apeglm
lfcshrink
5.7 years ago
coulsonr
▴ 20
5
votes
4
replies
2.0k
views
lfcShrink behavior with homogeneous expression dataset
deseq2
lfcshrink
betaprior
updated 5.7 years ago by
Michael Love
41k • written 5.7 years ago by
mat.lesche
▴ 90
22
votes
17
replies
7.1k
views
DESeq2 1.20.0 lfcshrink function
deseq2
differential expression
logfoldchange
lfcshrink
lfcthreshold
updated 2.9 years ago by
Michael Love
41k • written 5.8 years ago by
emi.sch
▴ 30
10
votes
6
replies
5.3k
views
Log2FoldChange shrinkage method in DESeq2
deseq2
apeglm
lfcshrink
updated 5.9 years ago by
Michael Love
41k • written 5.9 years ago by
Benjamin Ostendorf
▴ 90
0
votes
1
reply
1.3k
views
DESeq2::lfcshrink() for complex contrast designs
deseq2
lfcshrink
interaction term
updated 5.9 years ago by
Michael Love
41k • written 5.9 years ago by
krutherford
• 0
2
votes
4
replies
1.9k
views
DESeq2 with multi level
deseq2
lfcshrink
updated 6.0 years ago by
Michael Love
41k • written 6.0 years ago by
pierre.k
• 0
0
votes
3
replies
5.4k
views
How are the shrunk result data used in DESeq2?
deseq2
lfcshrink
updated 6.1 years ago by
Michael Love
41k • written 6.1 years ago by
thkapell
▴ 10
1
vote
2
replies
886
views
DESeq2 lfcShrink time for analysis
deseq2
lfcshrink
updated 6.2 years ago by
ellascottgm
• 0 • written 6.2 years ago by
jshouse
▴ 10
1
vote
12
replies
3.9k
views
DESeq2 LFC shrinkage is for designs with interactions
deseq2
lfcshrink
6.3 years ago
yk.gatc
• 0
3
votes
19
replies
5.6k
views
lfcShrink and factors with multiple levels
deseq2
lfcshrink
relevel
updated 6.4 years ago by
Michael Love
41k • written 6.4 years ago by
mat.lesche
▴ 90
1
vote
1
reply
1.2k
views
DESeq2 parallel argument for lfcShrink
deseq2
lfcshrink
updated 6.5 years ago by
Michael Love
41k • written 6.5 years ago by
dsull
• 0
0
votes
9
replies
1.8k
views
lfcshrink and rlog take forever to compute with a DESeqDataSet with many genotypes and conditions
deseq2
lfcshrink
rlog
6.6 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 6.7 years ago by
James W. MacDonald
65k • written 6.7 years ago by
tarun2
• 0
1
vote
4
replies
2.1k
views
Error when using lfcShrink and contrast argument in DESeq2
deseq2
lfcshrink
6.7 years ago
Oskar
▴ 50
0
votes
1
reply
1.3k
views
lfcShrink-coef option. Desired coefficient not appearing.
deseq2
lfcShrink
updated 6.7 years ago by
Michael Love
41k • written 6.7 years ago by
Victor Barrera
• 0
46 results • Page
1 of 1
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Replies
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.
Comment: 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…
Comment: get BM error
by
Fara
• 0
Thank you for your response. The primary reason for translating Ensembl IDs into Entrez Gene IDs is to perform KEGG (Kyoto Encyclopedia of…
Comment: Error for AnnotationForge makeOrgPackageFromNCBI function
by
James W. MacDonald
65k
That's weird. I don't have any problem at all generating the `OrgDb` on my box. How big is the gene2pubmed.gz file? I get this: ``` gzip -…
Votes
Answer: get BM error
Answer: Use of negative binomial model for exponential decay rate estimation using DESeq
Comment: Different Shrunk Log2FC according with reference
Reproducibility issue with scran together with lapply and BiocParallel
C: SGSeq: moving toward diffex from SGSeq analysis
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