Showing : apeglm • reset
5
votes
10
replies
1.2k
views
Allelic imbalance in apeglm
apeglm Allelic imbalance concept
updated 3.7 years ago by 42k • written 3.7 years ago by • 0
2
votes
7
replies
1.9k
views
optimHess problem in apeglm/DESeq2
DESeq2 apeglm
updated 12 months ago by 42k • written 12 months ago by ★ 4.1k
10
votes
6
replies
5.3k
views
Log2FoldChange shrinkage method in DESeq2
deseq2 apeglm lfcshrink
updated 6.0 years ago by 42k • written 6.0 years ago by ▴ 90
1
vote
5
replies
1.9k
views
DESeq2 outlier options and LFC Shrinkage
DESeq2 RNASeq RnaSeqSampleSize apeglm
updated 21 months ago by 42k • written 21 months ago by • 0
1
vote
5
replies
1.4k
views
lfcShrink probelm in many 0 count genes RNA-seq data
ashr DESeq2 apeglm
updated 2.7 years ago by 42k • written 2.7 years ago by ▴ 40
1
vote
4
replies
1.7k
views
Using different LFC shrinkage estimators for spike-in normalised RNA-seq data
deseq2 apeglm rna-seq spike-in
updated 3.7 years ago by 42k • written 3.7 years ago by ▴ 10
0
votes
4
replies
1.1k
views
Error in Apeglm Method for Effect Size Shrinkage
deseq2 apeglm
updated 5.9 years ago by 42k • written 5.9 years ago by ▴ 40
4
votes
4
replies
2.1k
views
Unexpected MAplot after apeglm shrinkage in DESeq2
apeglm deseq2 rna-seq
updated 5.5 years ago by 42k • written 5.5 years ago by ★ 4.1k
2
votes
4
replies
1.3k
views
What is the biological meaning of genes with FC = 0 after shrinkage
deseq2 apeglm
updated 5.1 years ago by 42k • written 5.1 years ago by • 0
3
votes
4
replies
2.2k
views
Reporting S values? Reporting padj values?
deseq2 apeglm
updated 3.9 years ago by 42k • written 3.9 years ago by ▴ 20
4
votes
4
replies
2.5k
views
RNA seq analysis using Deseq2 and apeglm lfc shrinkage
deseq2 fdrtool apeglm
updated 4.1 years ago by 42k • written 4.1 years 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
0
votes
4
replies
667
views
lfc direction of effect flipped for ashr, apeGLM, but accurate to biological data for non-shrunken
DESeq2 apeglm DESeq ApeGLM Ashr
updated 9 months ago by 42k • written 9 months ago by ▴ 20
1
vote
3
replies
1.6k
views
Choosing an svalue threshold from apeglm shrunken results in DESeq2
apeglm DESeq2
updated 2.7 years ago by 42k • written 2.7 years ago by ▴ 40
0
votes
3
replies
1.0k
views
Using altHypothesis on apleglm-shrunken log2FoldChanges
apeglm DESeq2
3.3 years ago zefrieira • 0
3
votes
3
replies
1.4k
views
Using alternative LFC shrinkage methods for computing p-values in DESeq2
deseq2 apeglm statistics
updated 4.9 years ago by 42k • written 4.9 years ago by • 0
0
votes
3
replies
667
views
Influence of DEG in ASE analysis within apeglm
apeglm
updated 3.6 years ago by 42k • written 3.6 years ago by • 0
1
vote
3
replies
993
views
LFC shrinkage setting negative LFC svalues to zero
DESeq2 DifferentialExpression apeglm
updated 22 months ago by 42k • written 22 months ago by • 0
1
vote
2
replies
1.2k
views
Use of shrunken LFCs to address questions about the distribution of LFCs between gene categories.
deseq2 apeglm DESeq2
2.3 years ago i.sudbery ▴ 40
0
votes
2
replies
842
views
running apeglm on a normal model and multiple coefficients
shrinkage apeglm
2.0 years ago Frederik Ziebell ▴ 20
0
votes
2
replies
848
views
Error: insufficient numeric precision during Log fold change shrinkage with apeglm
apeglm
updated 8 months ago by 42k • written 8 months ago by • 0
0
votes
2
replies
1.2k
views
lfcShrink in DESeq2
deseq2 apeglm
updated 4.8 years ago by 42k • written 4.8 years ago by • 0
0
votes
2
replies
946
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
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
3
votes
2
replies
1.9k
views
lfcShrink function in DEseq2 and s-values
deseq2 apeglm
updated 3.7 years ago by 42k • written 3.7 years ago by ▴ 10
0
votes
2
replies
2.7k
views
DESeq2 coefficients for APEGLM-shrinkage
deseq2 apeglm
updated 5.5 years ago by 42k • written 5.5 years ago by • 0
0
votes
2
replies
1.3k
views
DSEQ apeglm
DESeq2 apeglm
3.3 years ago amoaristotle ▴ 10
2
votes
2
replies
1.1k
views
DESeq2 in R
DESeq2 apeglm
updated 3.3 years ago by ★ 1.4k • written 3.3 years ago by ▴ 10
3
votes
2
replies
1.4k
views
Calculate S/N ratios from apeglm for GSEA
apeglm fgsea Signal-To-Noise Ratio
updated 5.0 years ago by 42k • written 5.0 years ago by ▴ 20
3
votes
2
replies
804
views
DESeq2 lfcShrink: swapping reference gives different results for the same comparison
DESeq2 apeglm
13 months ago Daphnia • 0
0
votes
1
reply
199
views
lfcShrink error: the line search routine failed
apeglm DESeq2
updated 7 weeks ago by 42k • written 7 weeks ago by • 0
2
votes
1
reply
975
views
Deactivate svalue=T in lfcShrink - DESeq2 - apeglm
deseq2 apeglm
updated 5.1 years ago by 42k • written 5.1 years ago by ★ 4.1k
1
vote
1
reply
804
views
Why s-values instead of p-values with non-default lfcThreshold and apeglm shrinkage in DESeq2
deseq2 apeglm
updated 3.9 years ago by 42k • written 3.9 years ago by • 0
2
votes
1
reply
674
views
What are the steps to use a complex model of Allelic imbalance through apeglm
apeglm complex model ASE Allelic imbalance
updated 3.8 years ago by 42k • written 3.8 years ago by • 0
1
vote
1
reply
629
views
Exceeding Over-dispersion parameter bbEstDisp
apeglm bbEstdisp allele ratio
updated 3.7 years ago by 42k • written 3.7 years ago by • 0
0
votes
1
reply
951
views
DESeq2 - shrunken LFC calculation
apeglm DESeq2
updated 3.3 years ago by 42k • written 3.3 years ago by ▴ 50
2
votes
1
reply
1.1k
views
apeglm -- influence of reference level on logFC and svalues
DESeq2 apeglm
updated 3.3 years ago by 42k • written 3.3 years ago by ★ 4.1k
0
votes
1
reply
981
views
Plotting the most expressed genes after conducting DESeq2
DESeq2 pheatmap apeglm
updated 3.2 years ago by 42k • written 3.2 years ago by ▴ 10
0
votes
1
reply
708
views
Non-significant but high LFC after apeglm shrinkage
DESeq2 apeglm
updated 3.2 years ago by 42k • written 3.2 years ago by • 0
39 results • Page 1 of 1
Recent ...
Replies
Answer: Differential gene expression analysis results by ATpoint ★ 4.1k
Pease do not open multiple posts for the same issue: https://support.bioconductor.org/p/9158194/#9158222 The support site is not meant f…
Comment: deseq2 results by sajadahmad41454 • 0
thank you for your response, should i remove or discard that sample? since the red outlier on left represents one of healthy samples.
Comment: deseq2 results by swbarnes2 ★ 1.4k
It looks like the PCA plot of a real RNASeq experiment. The red outlier on the left might be the mathematical reason why you have few vali…
Comment: Multi-factorial, longitudinal disease progression analysis with unbalanced patie by Dylan.Sheerin • 0
Thank you very much, Gordon. I'll give voomLmFit a go!
Answer: Multi-factorial, longitudinal disease progression analysis with unbalanced patie by Gordon Smyth 50k
Including subjectID in the design matrix always accounts for unbalanced sampling and patient variation but subjects with incomplete records…
Votes
Comment: deseq2 results
Comment: deseq2 results
Answer: Multi-factorial, longitudinal disease progression analysis with unbalanced patie
Answer: Extremely small p-values using Limma for proteomic data
Bioconductor 3.19 is Released!
Awards • All
Popular Question to Pietro ▴ 40
Popular Question to neilzhao ▴ 30
Popular Question to ATpoint ★ 4.1k
Teacher to Michael Love 42k
Popular Question to Haibo Liu • 0
Locations • All
Spain, 4 minutes ago
EMBL Heidelberg, 6 minutes ago
Italy, 7 minutes ago
France/Marseille/Inserm, 10 minutes ago
France, 12 minutes ago
Traffic: 625 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