Showing : lfcShrink • reset
22
votes
17
replies
7.2k
views
DESeq2 1.20.0 lfcshrink function
deseq2 differential expression logfoldchange lfcshrink lfcthreshold
updated 3.0 years ago by 42k • written 5.9 years ago by ▴ 30
10
votes
6
replies
5.4k
views
Log2FoldChange shrinkage method in DESeq2
deseq2 apeglm lfcshrink
updated 6.0 years ago by 42k • written 6.0 years ago by ▴ 90
5
votes
4
replies
2.1k
views
lfcShrink behavior with homogeneous expression dataset
deseq2 lfcshrink betaprior
updated 5.8 years ago by 42k • written 5.8 years ago by ▴ 90
4
votes
1
reply
1.1k
views
DEGs from lfcshrink() and results()
lfcshrink DESeq2
updated 2.3 years ago by ★ 4.1k • written 2.3 years ago by ▴ 10
4
votes
2
replies
2.6k
views
Interpreting the results from lfcShrink() with apeglm in DESeq2
deseq2 apeglm lfcshrink
updated 5.6 years ago by 42k • written 5.6 years ago by ▴ 160
4
votes
4
replies
840
views
DESeq2 lfcShrink function used in DiffBind package
FoldChange DiffBind lfcShrink Cut&TagData
11 months ago • updated 10 months ago bhandary.8590 ▴ 20
3
votes
4
replies
885
views
lfcShrink() and batch effects in DESeq2
BatchEffect lfcshrink RNA-seq DESeq2
9 months ago Eva ▴ 10
3
votes
3
replies
1.1k
views
lfc shrinkage two factor experiment
deseq2 lfcShrink
updated 5.0 years ago by 42k • written 5.0 years ago by • 0
3
votes
19
replies
5.7k
views
lfcShrink and factors with multiple levels
deseq2 lfcshrink relevel
updated 6.5 years ago by 42k • written 6.5 years ago by ▴ 90
3
votes
5
replies
1.5k
views
lfcShrink, interactions, and ashr
deseq2 lfcshrink contrast
updated 5.4 years ago by 42k • written 5.4 years ago by ▴ 10
2
votes
17
replies
1.8k
views
lfcshrink error DESeq2
DESeq2 lfcshrink DESe
updated 12 months ago by 42k • written 12 months ago by • 0
2
votes
4
replies
2.4k
views
ashr vs apeglm for interaction data
lfcShrink DESeq2
24 months ago Ali Barry ▴ 40
2
votes
5
replies
2.8k
views
Error in lfcShrink
lfcShrink DESeq2
updated 3.5 years ago by ▴ 90 • written 3.5 years ago by • 0
2
votes
3
replies
1.9k
views
lfcshrink() with no coef in resultsNames()
lfcshrink coef DESeq2
updated 2.5 years ago by 42k • written 3.5 years ago by ★ 1.5k
2
votes
4
replies
1.9k
views
DESeq2 with multi level
deseq2 lfcshrink
updated 6.1 years ago by 42k • written 6.1 years ago by • 0
2
votes
2
replies
913
views
Negative svalues from DESeq2 lfcShrink with ashr
ashr DESeq2 lfcShrink svalue
3.2 years ago Enrico • 0
1
vote
3
replies
1.3k
views
Correct use of Likelihood Ratio Test and LFC Shrinkage
RNASeq LRT DESeq2 lfcShrink
updated 15 months ago by • 0 • written 2.3 years ago by • 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
1
vote
3
replies
906
views
Why are padj results different for BetaPrior = TRUE vs lfcShrink()?
IHW lfcShrink DESeq2
2.1 years ago Ali Barry ▴ 40
1
vote
12
replies
3.9k
views
DESeq2 LFC shrinkage is for designs with interactions
deseq2 lfcshrink
6.3 years ago yk.gatc • 0
1
vote
6
replies
1.5k
views
Zero pvalues after lfcShrink of DESeq2 package
deseq2 pvalue lfcshrink
updated 5.1 years ago by 42k • written 5.1 years ago by ▴ 10
1
vote
2
replies
1.7k
views
DEseq2 anlysis - LfcThreshold and Lfcshrink options
lfcshrink DESeq2 RNASeq lfcthreshold
22 months ago ClaudiaE • 0
1
vote
2
replies
906
views
DESeq2 lfcShrink time for analysis
deseq2 lfcshrink
updated 6.3 years ago by • 0 • written 6.3 years ago by ▴ 10
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 65k • written 6.7 years ago by • 0
1
vote
1
reply
25k
views
lfcShrink doesn't work with contrasts
lfcShrink contrast design deseq2
updated 4.3 years ago by 42k • written 4.3 years ago by ★ 1.5k
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
785
views
LFCshrink function understanding
deseq2 MAplot lfcshrink
updated 3.7 years ago by 42k • written 3.7 years ago by • 0
1
vote
1
reply
809
views
Identifying DEGs using lfcshrink()
DESeq2 lfcshrink
updated 19 months ago by 42k • written 19 months ago by ▴ 10
1
vote
1
reply
2.3k
views
Question regarding lfcShrink types in DiffBind
FoldChange DiffBind lfcShrink
updated 9 months ago by ★ 5.2k • written 10 months ago by ▴ 20
1
vote
3
replies
1.0k
views
resultsNames(dds) not showing all contrasts
DESeq2 resultsNames lfcShrink
updated 20 months ago by ★ 4.1k • written 20 months ago by • 0
1
vote
4
replies
1.6k
views
Log2 fold-change shrinkage fails with lfcShrink when using the 'apeglm' method
deseq2 apeglm lfcshrink
5.8 years ago coulsonr ▴ 20
1
vote
1
reply
1.2k
views
DESeq2 parallel argument for lfcShrink
deseq2 lfcshrink
updated 6.6 years ago by 42k • written 6.6 years ago by • 0
0
votes
2
replies
553
views
DESeq2 : stat or lfcshrink for GSEA analysis
lfcshrink GSEABenchmarkeR DESeq2
updated 5 months ago by ★ 4.1k • written 5 months ago by • 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
6.7 years ago pecot • 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 42k • written 6.1 years ago by ▴ 10
0
votes
1
reply
1.3k
views
DESeq2::lfcshrink() for complex contrast designs
deseq2 lfcshrink interaction term
updated 6.0 years ago by 42k • written 6.0 years ago by • 0
0
votes
2
replies
1.1k
views
lfcshrink in DESeq2 with grouping variable
deseq2 lfcshrink
updated 5.7 years ago by 42k • written 5.7 years ago by ▴ 10
0
votes
1
reply
1.1k
views
DESeq2 - shrunken log fold changes and threshold test
deseq2 lfcshrink lfcthreshold differential gene expression
updated 5.5 years ago by 42k • written 5.5 years ago by • 0
0
votes
4
replies
1.9k
views
DESeq2 lfcShrink with interactions
deseq2 lfcShrink interactions
updated 5.3 years ago by 42k • written 5.3 years ago by • 0
0
votes
1
reply
849
views
DESeq2: three conditions lfcShrink CvsB analysis
deseq2 lfcShrink
updated 4.9 years ago by 42k • written 4.9 years ago by • 0
0
votes
2
replies
948
views
Coefficient names for multiple group comparisons to use with lfcShrink & apeglm
deseq2 lfcShrink apeglm
updated 4.4 years ago by 42k • written 4.4 years ago by ▴ 20
0
votes
3
replies
949
views
lfcShrink contrast
lfcshrink R DESeq2
updated 2.1 years ago by ★ 4.1k • written 2.1 years ago by • 0
0
votes
1
reply
747
views
Variation in number of DEGs on LFC shrinkage
DESeq2 lfcShrink
updated 2.5 years ago by 42k • written 2.5 years ago by • 0
0
votes
4
replies
700
views
Should I use the 'log2FoldChange' from lfcShrink() to subset significant DEGs?
lfcshrink DESeq2
written 4 months ago by • 0
0
votes
1
reply
716
views
lfcshrink() and 2 conditions, 3 genotypes
lfcshrink DESeq2
updated 2.5 years ago by 42k • written 2.5 years ago by • 0
0
votes
1
reply
1.3k
views
lfcShrink-coef option. Desired coefficient not appearing.
deseq2 lfcShrink
updated 6.8 years ago by 42k • written 6.8 years ago by • 0
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Comment: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa by alex.pico ▴ 20
Hi Matthew. Happy to help. The error message you are getting is indeed not very helpful. It's just saying that the CyREST return obj "res" …
Comment: ChipQC 'names' attribute [9] must be the same length as the vector [2]' by bandconductor • 0
thanks! you have saved me so much time
Comment: Problem finding certain variables when importing a public database GSE73103 by Guido Hooiveld ★ 3.9k
FWIW: when I would like to make use of publicly available data, I always use the website to explore which metadata is submitted to GEO (and…
Comment: How to use bootRanges to bootstrap small RNA loci (nullranges package) by Michael Love 42k
This is `blockLength=200000`, and providing `seg=seg`? It's alright that it's not identical. In the bootstrapped data, you will now have l…
Comment: How to use bootRanges to bootstrap small RNA loci (nullranges package) by Poonam • 0
Thank you, Michael. I used the script shared by you. The genomic distribution of the original and null loci looks like non-stationary. Plea…
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Answer: ChipQC 'names' attribute [9] must be the same length as the vector [2]'
ChipQC 'names' attribute [9] must be the same length as the vector [2]'
A: DEXSeq time course design
using variable in design formula
differential expression for Single-cell RNAseq data using edgeR
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