Showing : lfcshrink • reset
3
votes
19
replies
5.7k
views
lfcShrink and factors with multiple levels
deseq2 lfcshrink relevel
updated 6.5 years ago by 41k • written 6.5 years ago by ▴ 90
22
votes
17
replies
7.2k
views
DESeq2 1.20.0 lfcshrink function
deseq2 differential expression logfoldchange lfcshrink lfcthreshold
updated 2.9 years ago by 41k • written 5.9 years ago by ▴ 30
2
votes
17
replies
1.7k
views
lfcshrink error DESeq2
DESeq2 lfcshrink DESe
updated 11 months ago by 41k • written 12 months ago by • 0
1
vote
12
replies
3.9k
views
DESeq2 LFC shrinkage is for designs with interactions
deseq2 lfcshrink
6.3 years ago yk.gatc • 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 • updated 6.6 years ago pecot • 0
10
votes
6
replies
5.3k
views
Log2FoldChange shrinkage method in DESeq2
deseq2 apeglm lfcshrink
updated 6.0 years ago by 41k • written 6.0 years ago by ▴ 90
1
vote
6
replies
1.5k
views
Zero pvalues after lfcShrink of DESeq2 package
deseq2 pvalue lfcshrink
updated 5.1 years ago by 41k • written 5.1 years ago by ▴ 10
3
votes
5
replies
1.5k
views
lfcShrink, interactions, and ashr
deseq2 lfcshrink contrast
updated 5.4 years ago by 41k • written 5.4 years ago by ▴ 10
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
4
replies
1.9k
views
DESeq2 with multi level
deseq2 lfcshrink
updated 6.0 years ago by 41k • written 6.0 years ago by • 0
2
votes
4
replies
2.4k
views
ashr vs apeglm for interaction data
lfcShrink DESeq2
23 months ago Ali Barry ▴ 40
3
votes
4
replies
868
views
lfcShrink() and batch effects in DESeq2
BatchEffect lfcshrink RNA-seq DESeq2
8 months ago Eva ▴ 10
4
votes
4
replies
815
views
DESeq2 lfcShrink function used in DiffBind package
FoldChange DiffBind lfcShrink Cut&TagData
10 months ago bhandary.8590 ▴ 20
5
votes
4
replies
2.1k
views
lfcShrink behavior with homogeneous expression dataset
deseq2 lfcshrink betaprior
updated 5.8 years ago by 41k • written 5.8 years ago by ▴ 90
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 • updated 5.7 years ago coulsonr ▴ 20
0
votes
4
replies
679
views
Should I use the 'log2FoldChange' from lfcShrink() to subset significant DEGs?
lfcshrink DESeq2
written 4 months ago by • 0
0
votes
4
replies
1.9k
views
DESeq2 lfcShrink with interactions
deseq2 lfcShrink interactions
updated 5.3 years ago by 41k • written 5.3 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
892
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
5.4k
views
How are the shrunk result data used in DESeq2?
deseq2 lfcshrink
updated 6.1 years ago by 41k • written 6.1 years ago by ▴ 10
3
votes
3
replies
1.1k
views
lfc shrinkage two factor experiment
deseq2 lfcShrink
updated 5.0 years ago by 41k • written 5.0 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 41k • written 3.5 years ago by ★ 1.5k
0
votes
3
replies
940
views
lfcShrink contrast
lfcshrink R DESeq2
updated 2.1 years ago by ★ 4.1k • written 2.1 years ago by • 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
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
2
replies
895
views
DESeq2 lfcShrink time for analysis
deseq2 lfcshrink
updated 6.2 years ago by • 0 • written 6.2 years ago by ▴ 10
0
votes
2
replies
528
views
DESeq2 : stat or lfcshrink for GSEA analysis
lfcshrink GSEABenchmarkeR DESeq2
updated 4 months ago by ★ 4.1k • written 5 months ago by • 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 65k • written 6.7 years ago by • 0
1
vote
2
replies
1.7k
views
DEseq2 anlysis - LfcThreshold and Lfcshrink options
lfcshrink DESeq2 RNASeq lfcthreshold
22 months ago ClaudiaE • 0
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 41k • written 5.6 years ago by ▴ 160
0
votes
2
replies
1.1k
views
lfcshrink in DESeq2 with grouping variable
deseq2 lfcshrink
updated 5.7 years ago by 41k • written 5.7 years ago by ▴ 10
0
votes
2
replies
938
views
Coefficient names for multiple group comparisons to use with lfcShrink & apeglm
deseq2 lfcShrink apeglm
updated 4.4 years ago by 41k • written 4.4 years ago by ▴ 20
2
votes
2
replies
904
views
Negative svalues from DESeq2 lfcShrink with ashr
ashr DESeq2 lfcShrink svalue
3.2 years ago Enrico • 0
1
vote
1
reply
1.2k
views
DESeq2 parallel argument for lfcShrink
deseq2 lfcshrink
updated 6.5 years ago by 41k • written 6.5 years ago by • 0
0
votes
1
reply
1.1k
views
DESeq2 - shrunken log fold changes and threshold test
deseq2 lfcshrink lfcthreshold differential gene expression
updated 5.4 years ago by 41k • written 5.4 years ago by • 0
0
votes
1
reply
709
views
lfcshrink() and 2 conditions, 3 genotypes
lfcshrink DESeq2
updated 2.5 years ago by 41k • written 2.5 years ago by • 0
0
votes
1
reply
846
views
DESeq2: three conditions lfcShrink CvsB analysis
deseq2 lfcShrink
updated 4.9 years ago by 41k • written 4.9 years ago by • 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 41k • written 4.3 years ago by ★ 1.5k
1
vote
1
reply
775
views
LFCshrink function understanding
deseq2 MAplot lfcshrink
updated 3.7 years ago by 41k • written 3.7 years ago by • 0
1
vote
1
reply
2.2k
views
Question regarding lfcShrink types in DiffBind
FoldChange DiffBind lfcShrink
updated 9 months ago by ★ 5.2k • written 9 months ago by ▴ 20
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
1
vote
1
reply
795
views
Identifying DEGs using lfcshrink()
DESeq2 lfcshrink
updated 19 months ago by 41k • written 19 months ago by • 0
0
votes
1
reply
1.3k
views
lfcShrink-coef option. Desired coefficient not appearing.
deseq2 lfcShrink
updated 6.7 years ago by 41k • written 6.7 years ago by • 0
0
votes
1
reply
744
views
Variation in number of DEGs on LFC shrinkage
DESeq2 lfcShrink
updated 2.5 years ago by 41k • written 2.5 years ago by • 0
0
votes
1
reply
1.3k
views
DESeq2::lfcshrink() for complex contrast designs
deseq2 lfcshrink interaction term
updated 6.0 years ago by 41k • written 6.0 years ago by • 0
46 results • Page 1 of 1
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Answer: Once again a "Model matrix not full rank" by swbarnes2 ★ 1.3k
Replicate numbers, like the 1 in control_1 are fine in sample names, but never add them to anything else in colData. From the computer's p…
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I'll add a little bit of general advice to James' answer. You seem to have the misunderstanding that you can change the design matrix but …
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It is true that goseq isn't available for Bioc 3.19. That is because goseq depends on txbmaker, which is itself not yet available for Bioc…
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This part: ``` design_intercept <- model.matrix(~Alt+Sex+Age+PC1, data=targets_Sherpa) colnames(design_intercept) <- c("AltSHP_LA","Al…
Comment: CombineArrays for EPIC and EPIC V2 by Kim • 0
Thank you Tim, this is a great help in getting me started!
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Answer: limma Intercept vs No-intercept models completely changing DMR results?
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