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lfcShrink
•
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0
votes
4
replies
1.0k
views
Should I use the 'log2FoldChange' from lfcShrink() to subset significant DEGs?
lfcshrink
DESeq2
written 10 months ago by
Igor
• 0
0
votes
2
replies
1.1k
views
DESeq2 : stat or lfcshrink for GSEA analysis
lfcshrink
GSEABenchmarkeR
DESeq2
updated 11 months ago by
ATpoint
★ 4.5k • written 11 months ago by
delphine.rossille
• 0
3
votes
4
replies
1.2k
views
lfcShrink() and batch effects in DESeq2
BatchEffect
lfcshrink
RNA-seq
DESeq2
15 months ago
Eva
▴ 10
1
vote
1
reply
3.8k
views
Question regarding lfcShrink types in DiffBind
FoldChange
DiffBind
lfcShrink
updated 15 months ago by
Rory Stark
★ 5.2k • written 16 months ago by
bhandary.8590
▴ 20
4
votes
4
replies
1.2k
views
DESeq2 lfcShrink function used in DiffBind package
FoldChange
DiffBind
lfcShrink
Cut&TagData
16 months ago
bhandary.8590
▴ 20
2
votes
17
replies
2.3k
views
lfcshrink error DESeq2
DESeq2
lfcshrink
DESe
updated 18 months ago by
Michael Love
42k • written 18 months ago by
Alina
• 0
3
votes
1
reply
1.0k
views
Identifying DEGs using lfcshrink()
DESeq2
lfcshrink
updated 2.1 years ago by
Michael Love
42k • written 2.1 years ago by
Zainab
▴ 20
1
vote
3
replies
1.3k
views
resultsNames(dds) not showing all contrasts
DESeq2
resultsNames
lfcShrink
updated 2.2 years ago by
ATpoint
★ 4.5k • written 2.2 years ago by
eve.olszanowski
• 0
1
vote
2
replies
2.2k
views
DEseq2 anlysis - LfcThreshold and Lfcshrink options
lfcshrink
DESeq2
RNASeq
lfcthreshold
2.3 years ago
ClaudiaE
• 0
2
votes
4
replies
3.0k
views
ashr vs apeglm for interaction data
lfcShrink
DESeq2
2.5 years ago
Ali Barry
▴ 40
1
vote
3
replies
1.1k
views
Why are padj results different for BetaPrior = TRUE vs lfcShrink()?
IHW
lfcShrink
DESeq2
2.5 years ago
Ali Barry
▴ 40
0
votes
3
replies
1.2k
views
lfcShrink contrast
lfcshrink
R
DESeq2
updated 2.6 years ago by
ATpoint
★ 4.5k • written 2.6 years ago by
LHA_trash
• 0
4
votes
1
reply
1.3k
views
DEGs from lfcshrink() and results()
lfcshrink
DESeq2
updated 2.8 years ago by
ATpoint
★ 4.5k • written 2.8 years ago by
BT
▴ 10
1
vote
3
replies
1.6k
views
Correct use of Likelihood Ratio Test and LFC Shrinkage
RNASeq
LRT
DESeq2
lfcShrink
updated 21 months ago by
ayabalbaa1990
• 0 • written 2.8 years ago by
Emma
• 0
0
votes
1
reply
859
views
Variation in number of DEGs on LFC shrinkage
DESeq2
lfcShrink
updated 3.0 years ago by
Michael Love
42k • written 3.0 years ago by
Deevanshu
• 0
0
votes
1
reply
842
views
lfcshrink() and 2 conditions, 3 genotypes
lfcshrink
DESeq2
updated 3.0 years ago by
Michael Love
42k • written 3.0 years ago by
Nayrouz
• 0
2
votes
2
replies
1.1k
views
Negative svalues from DESeq2 lfcShrink with ashr
ashr
DESeq2
lfcShrink
svalue
3.7 years ago
Enrico
• 0
2
votes
5
replies
3.3k
views
Error in lfcShrink
lfcShrink
DESeq2
updated 4.0 years ago by
tcalvo
▴ 100 • written 4.0 years ago by
Claudio Carril
• 0
2
votes
3
replies
2.3k
views
lfcshrink() with no coef in resultsNames()
lfcshrink
coef
DESeq2
updated 3.0 years ago by
Michael Love
42k • written 4.0 years ago by
Assa Yeroslaviz
★ 1.5k
1
vote
1
reply
923
views
LFCshrink function understanding
deseq2
MAplot
lfcshrink
updated 4.2 years ago by
Michael Love
42k • written 4.2 years ago by
evelas13
• 0
1
vote
1
reply
22k
views
Why does the DESEQ2 lfcshrink function results not include the stat variable
deseq2
stat
lfcshrink
4.6 years ago
divercory
• 0
1
vote
1
reply
27k
views
lfcShrink doesn't work with contrasts
lfcShrink
contrast
design
deseq2
updated 4.8 years ago by
Michael Love
42k • written 4.8 years ago by
Assa Yeroslaviz
★ 1.5k
0
votes
2
replies
1.1k
views
Coefficient names for multiple group comparisons to use with lfcShrink & apeglm
deseq2
lfcShrink
apeglm
updated 4.9 years ago by
Michael Love
42k • written 4.9 years ago by
coulsonr
▴ 20
26
votes
17
replies
8.2k
views
DESeq2 1.20.0 lfcshrink function
deseq2
differential expression
logfoldchange
lfcshrink
lfcthreshold
updated 3.4 years ago by
Michael Love
42k • written 6.4 years ago by
emi.sch
▴ 40
0
votes
1
reply
987
views
DESeq2: three conditions lfcShrink CvsB analysis
deseq2
lfcShrink
updated 5.4 years ago by
Michael Love
42k • written 5.4 years ago by
kcbauer
• 0
3
votes
3
replies
1.3k
views
lfc shrinkage two factor experiment
deseq2
lfcShrink
updated 5.5 years ago by
Michael Love
42k • written 5.5 years ago by
rbutler
• 0
1
vote
6
replies
1.8k
views
Zero pvalues after lfcShrink of DESeq2 package
deseq2
pvalue
lfcshrink
updated 5.6 years ago by
Michael Love
42k • written 5.6 years ago by
peibo_xu
▴ 10
0
votes
4
replies
2.2k
views
DESeq2 lfcShrink with interactions
deseq2
lfcShrink
interactions
updated 5.8 years ago by
Michael Love
42k • written 5.8 years ago by
hannepainter
• 0
3
votes
5
replies
1.7k
views
lfcShrink, interactions, and ashr
deseq2
lfcshrink
contrast
updated 5.9 years ago by
Michael Love
42k • written 5.9 years ago by
jurbach
▴ 10
0
votes
1
reply
1.2k
views
DESeq2 - shrunken log fold changes and threshold test
deseq2
lfcshrink
lfcthreshold
differential gene expression
updated 6.0 years ago by
Michael Love
42k • written 6.0 years ago by
corentinrichard374369
• 0
4
votes
2
replies
2.8k
views
Interpreting the results from lfcShrink() with apeglm in DESeq2
deseq2
apeglm
lfcshrink
updated 6.1 years ago by
Michael Love
42k • written 6.1 years ago by
charles.foster
▴ 160
0
votes
2
replies
1.3k
views
lfcshrink in DESeq2 with grouping variable
deseq2
lfcshrink
updated 6.2 years ago by
Michael Love
42k • written 6.2 years ago by
kendralec
▴ 10
1
vote
4
replies
1.8k
views
Log2 fold-change shrinkage fails with lfcShrink when using the 'apeglm' method
deseq2
apeglm
lfcshrink
6.3 years ago
coulsonr
▴ 20
5
votes
4
replies
2.3k
views
lfcShrink behavior with homogeneous expression dataset
deseq2
lfcshrink
betaprior
updated 6.3 years ago by
Michael Love
42k • written 6.3 years ago by
mat.lesche
▴ 110
10
votes
6
replies
6.2k
views
Log2FoldChange shrinkage method in DESeq2
deseq2
apeglm
lfcshrink
updated 6.5 years ago by
Michael Love
42k • written 6.5 years ago by
Benjamin Ostendorf
▴ 90
0
votes
1
reply
1.5k
views
DESeq2::lfcshrink() for complex contrast designs
deseq2
lfcshrink
interaction term
updated 6.5 years ago by
Michael Love
42k • written 6.5 years ago by
krutherford
• 0
2
votes
4
replies
2.1k
views
DESeq2 with multi level
deseq2
lfcshrink
updated 6.5 years ago by
Michael Love
42k • written 6.5 years ago by
pierre.k
• 0
0
votes
3
replies
5.9k
views
How are the shrunk result data used in DESeq2?
deseq2
lfcshrink
updated 6.6 years ago by
Michael Love
42k • written 6.6 years ago by
thkapell
▴ 10
1
vote
2
replies
1.0k
views
DESeq2 lfcShrink time for analysis
deseq2
lfcshrink
updated 6.7 years ago by
ellascottgm
• 0 • written 6.7 years ago by
jshouse
▴ 10
1
vote
12
replies
4.2k
views
DESeq2 LFC shrinkage is for designs with interactions
deseq2
lfcshrink
6.8 years ago
yk.gatc
• 0
5
votes
19
replies
6.3k
views
lfcShrink and factors with multiple levels
deseq2
lfcshrink
relevel
updated 7.0 years ago by
Michael Love
42k • written 7.0 years ago by
mat.lesche
▴ 110
1
vote
1
reply
1.3k
views
DESeq2 parallel argument for lfcShrink
deseq2
lfcshrink
updated 7.0 years ago by
Michael Love
42k • written 7.0 years ago by
dsull
• 0
0
votes
9
replies
2.1k
views
lfcshrink and rlog take forever to compute with a DESeqDataSet with many genotypes and conditions
deseq2
lfcshrink
rlog
7.2 years ago • updated 7.1 years ago
pecot
• 0
1
vote
2
replies
1.7k
views
DESeq2 version 1.16.1 installation and difference with version 1.14.1
deseq2
betaprior=true
lfcshrink
updated 7.2 years ago by
James W. MacDonald
67k • written 7.2 years ago by
tarun2
• 0
1
vote
4
replies
2.3k
views
Error when using lfcShrink and contrast argument in DESeq2
deseq2
lfcshrink
7.2 years ago
Oskar
▴ 50
0
votes
1
reply
1.4k
views
lfcShrink-coef option. Desired coefficient not appearing.
deseq2
lfcShrink
updated 7.2 years ago by
Michael Love
42k • written 7.2 years ago by
Victor Barrera
• 0
46 results • Page
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Comment: Combining RNAseq and microarray data using edgeR/limma-voom
by
Adam Marstrand
• 0
Hi again, Thank you for the response! Can you expound on why it is not a good idea? I realize that the expression levels/differential expr…
Answer: Combining RNAseq and microarray data using edgeR/limma-voom
by
James W. MacDonald
67k
No, that's not a good idea at all. You should be doing a meta-analysis with these data rather than trying to combine like that. `GeneMeta` …
Answer: GOstats kegg analysis in wheat - help - none of the objects in the first column
by
James W. MacDonald
67k
Check the help page for `KEGGFrame`. Your columns are out of order.
Comment: Question about using LRT test for time course experiments with DESeq2
by
James W. MacDonald
67k
You are testing the interaction, so you are asking for those genes that change at any time *differently, depending on the treatment*. If co…
Comment: DESeq Input from Salmon + tximport/tximeta
by
LuciaNhu
• 0
Thank you both. Special thanks from Prof. Michael Love. It's rare to find tool authors who respond to users so quickly and supportively. Ma…
Votes
Comment: DESeq Input from Salmon + tximport/tximeta
Comment: DESeq Input from Salmon + tximport/tximeta
Comment: DESeq Input from Salmon + tximport/tximeta
Answer: DESeq Input from Salmon + tximport/tximeta
Answer: featureCounts segmentation fault with large chromosomes
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