Showing : lfcshrink • reset
0
votes
4
replies
682
views
Should I use the 'log2FoldChange' from lfcShrink() to subset significant DEGs?
lfcshrink DESeq2
written 4 months ago by • 0
0
votes
2
replies
529
views
DESeq2 : stat or lfcshrink for GSEA analysis
lfcshrink GSEABenchmarkeR DESeq2
updated 4 months ago by ★ 4.1k • written 5 months ago by • 0
3
votes
4
replies
871
views
lfcShrink() and batch effects in DESeq2
BatchEffect lfcshrink RNA-seq DESeq2
9 months ago • updated 8 months ago Eva ▴ 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 9 months ago by ▴ 20
4
votes
4
replies
817
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 41k • written 12 months ago by • 0
1
vote
1
reply
795
views
Identifying DEGs using lfcshrink()
DESeq2 lfcshrink
updated 19 months ago by 41k • written 19 months 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
1.7k
views
DEseq2 anlysis - LfcThreshold and Lfcshrink options
lfcshrink DESeq2 RNASeq lfcthreshold
22 months ago ClaudiaE • 0
2
votes
4
replies
2.4k
views
ashr vs apeglm for interaction data
lfcShrink DESeq2
23 months ago Ali Barry ▴ 40
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
941
views
lfcShrink contrast
lfcshrink R DESeq2
updated 2.1 years ago by ★ 4.1k • written 2.1 years ago by • 0
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
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
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
709
views
lfcshrink() and 2 conditions, 3 genotypes
lfcshrink DESeq2
updated 2.5 years ago by 41k • written 2.5 years ago by • 0
2
votes
2
replies
905
views
Negative svalues from DESeq2 lfcShrink with ashr
ashr DESeq2 lfcShrink svalue
3.2 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 41k • written 3.5 years ago by ★ 1.5k
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
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
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
0
votes
2
replies
939
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
1
vote
2
replies
896
views
DESeq2 lfcShrink time for analysis
deseq2 lfcshrink
updated 6.2 years ago by • 0 • written 6.2 years ago by ▴ 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
5.7k
views
lfcShrink and factors with multiple levels
deseq2 lfcshrink relevel
updated 6.5 years ago by 41k • written 6.5 years ago by ▴ 90
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
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
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
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 41k • written 6.7 years ago by • 0
46 results • Page 1 of 1
Recent ...
Replies
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…
Answer: limma Intercept vs No-intercept models completely changing DMR results? by Gordon Smyth 50k
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 …
Answer: package goseq seems to be not available on the latest version of R by Gordon Smyth 50k
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…
Answer: limma Intercept vs No-intercept models completely changing DMR results? by James W. MacDonald 65k
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!
Votes
Answer: Why does GSEA on edgeR results for randomized samples give highly significant p-
Answer: limma Intercept vs No-intercept models completely changing DMR results?
Answer: CombineArrays for EPIC and EPIC V2
Answer: Too many significant genes when integrating gtex and tcga
Comment: Too many significant genes when integrating gtex and tcga
Awards • All
Popular Question to Gordon Smyth 50k
Popular Question to Zainab • 0
Popular Question to Theo ▴ 10
Popular Question to gene_bioconductor ▴ 10
Popular Question to rohitsatyam102 ▴ 20
Locations • All
United States, 1 minute ago
United States, 8 minutes ago
United States, 30 minutes ago
France, 30 minutes ago
United States, 40 minutes ago
Traffic: 586 users visited in the last hour
Content Search
Users
Tags
Badges
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6