Showing : apeglm • reset
3
votes
1
reply
321
views
DESeq2 Apeglm Coefficient Reordering / Log2FoldChange Comparison Change
DESeq2 apeglm
updated 3 days ago by 68k • written 4 days ago by • 0
1
vote
2
replies
494
views
Questions in Regards to LFC shrinkage in DESeq2
Dseq2 RNASeqData apeglm
8 months ago Gordon • 0
2
votes
10
replies
1.2k
views
How to run allelic imbalance in apeglm
apeglm
12 months ago • updated 11 months ago euge.eugenio ▴ 20
0
votes
1
reply
1.3k
views
lfcShrink error: the line search routine failed
apeglm DESeq2
updated 14 months ago by 43k • written 14 months ago by • 0
0
votes
2
replies
1.8k
views
Error: insufficient numeric precision during Log fold change shrinkage with apeglm
apeglm
updated 20 months ago by 43k • written 21 months ago by • 0
0
votes
4
replies
1.1k
views
lfc direction of effect flipped for ashr, apeGLM, but accurate to biological data for non-shrunken
DESeq2 apeglm DESeq ApeGLM Ashr
updated 22 months ago by 43k • written 22 months ago by ▴ 20
2
votes
7
replies
2.7k
views
optimHess problem in apeglm/DESeq2
DESeq2 apeglm
updated 2.0 years ago by 43k • written 2.0 years ago by ★ 4.8k
3
votes
2
replies
1.3k
views
DESeq2 lfcShrink: swapping reference gives different results for the same comparison
DESeq2 apeglm
2.1 years ago Daphnia • 0
1
vote
5
replies
2.8k
views
DESeq2 outlier options and LFC Shrinkage
DESeq2 RNASeq RnaSeqSampleSize apeglm
updated 2.8 years ago by 43k • written 2.8 years ago by • 0
1
vote
3
replies
1.4k
views
LFC shrinkage setting negative LFC svalues to zero
DESeq2 DifferentialExpression apeglm
updated 2.8 years ago by 43k • written 2.8 years ago by • 0
1
vote
2
replies
1.3k
views
running apeglm on a normal model and multiple coefficients
shrinkage apeglm
3.1 years ago Frederik Ziebell ▴ 30
1
vote
2
replies
1.6k
views
Use of shrunken LFCs to address questions about the distribution of LFCs between gene categories.
deseq2 apeglm DESeq2
3.3 years ago i.sudbery ▴ 40
2
votes
3
replies
2.4k
views
Choosing an svalue threshold from apeglm shrunken results in DESeq2
apeglm DESeq2
updated 3.7 years ago by 43k • written 3.7 years ago by ▴ 40
1
vote
5
replies
2.0k
views
lfcShrink probelm in many 0 count genes RNA-seq data
ashr DESeq2 apeglm
updated 3.7 years ago by 43k • written 3.8 years ago by ▴ 40
0
votes
1
reply
937
views
Non-significant but high LFC after apeglm shrinkage
DESeq2 apeglm
updated 4.2 years ago by 43k • written 4.2 years ago by • 0
0
votes
1
reply
1.5k
views
Plotting the most expressed genes after conducting DESeq2
DESeq2 pheatmap apeglm
updated 4.3 years ago by 43k • written 4.3 years ago by ▴ 10
2
votes
2
replies
1.5k
views
DESeq2 in R
DESeq2 apeglm
updated 4.3 years ago by ★ 1.4k • written 4.3 years ago by ▴ 10
0
votes
2
replies
1.6k
views
DSEQ apeglm
DESeq2 apeglm
4.3 years ago amoaristotle ▴ 10
2
votes
1
reply
1.6k
views
apeglm -- influence of reference level on logFC and svalues
DESeq2 apeglm
updated 4.3 years ago by 43k • written 4.3 years ago by ★ 4.8k
0
votes
3
replies
1.3k
views
Using altHypothesis on apleglm-shrunken log2FoldChanges
apeglm DESeq2
4.4 years ago zefrieira • 0
0
votes
1
reply
1.3k
views
DESeq2 - shrunken LFC calculation
apeglm DESeq2
updated 4.4 years ago by 43k • written 4.4 years ago by ▴ 50
0
votes
3
replies
933
views
Influence of DEG in ASE analysis within apeglm
apeglm
updated 4.6 years ago by 43k • written 4.6 years ago by • 0
1
vote
1
reply
879
views
Exceeding Over-dispersion parameter bbEstDisp
apeglm bbEstdisp allele ratio
updated 4.7 years ago by 43k • written 4.7 years ago by • 0
5
votes
10
replies
1.8k
views
Allelic imbalance in apeglm
apeglm Allelic imbalance concept
updated 4.7 years ago by 43k • written 4.7 years ago by • 0
1
vote
4
replies
2.3k
views
Using different LFC shrinkage estimators for spike-in normalised RNA-seq data
deseq2 apeglm rna-seq spike-in
updated 4.8 years ago by 43k • written 4.8 years ago by ▴ 10
3
votes
2
replies
2.7k
views
lfcShrink function in DEseq2 and s-values
deseq2 apeglm
updated 4.8 years ago by 43k • written 4.8 years ago by ▴ 10
2
votes
1
reply
957
views
What are the steps to use a complex model of Allelic imbalance through apeglm
apeglm complex model ASE Allelic imbalance
updated 4.8 years ago by 43k • written 4.8 years ago by • 0
1
vote
1
reply
1.2k
views
Why s-values instead of p-values with non-default lfcThreshold and apeglm shrinkage in DESeq2
deseq2 apeglm
updated 4.9 years ago by 43k • written 4.9 years ago by • 0
3
votes
4
replies
2.7k
views
Reporting S values? Reporting padj values?
deseq2 apeglm
updated 4.9 years ago by 43k • written 4.9 years ago by ▴ 20
4
votes
4
replies
3.6k
views
RNA seq analysis using Deseq2 and apeglm lfc shrinkage
deseq2 fdrtool apeglm
updated 5.1 years ago by 43k • written 5.1 years ago by • 0
0
votes
2
replies
1.3k
views
Coefficient names for multiple group comparisons to use with lfcShrink & apeglm
deseq2 lfcShrink apeglm
updated 5.4 years ago by 43k • written 5.4 years ago by ▴ 20
0
votes
2
replies
1.6k
views
lfcShrink in DESeq2
deseq2 apeglm
updated 5.8 years ago by 43k • written 5.8 years ago by • 0
3
votes
3
replies
1.9k
views
Using alternative LFC shrinkage methods for computing p-values in DESeq2
deseq2 apeglm statistics
updated 6.0 years ago by 43k • written 6.0 years ago by • 0
3
votes
2
replies
2.0k
views
Calculate S/N ratios from apeglm for GSEA
apeglm fgsea Signal-To-Noise Ratio
updated 6.0 years ago by 43k • written 6.0 years ago by ▴ 20
2
votes
1
reply
1.2k
views
Deactivate svalue=T in lfcShrink - DESeq2 - apeglm
deseq2 apeglm
updated 6.1 years ago by 43k • written 6.1 years ago by ★ 4.8k
2
votes
4
replies
1.8k
views
What is the biological meaning of genes with FC = 0 after shrinkage
deseq2 apeglm
updated 6.2 years ago by 43k • written 6.2 years ago by • 0
0
votes
2
replies
3.4k
views
DESeq2 coefficients for APEGLM-shrinkage
deseq2 apeglm
updated 6.5 years ago by 43k • written 6.5 years ago by • 0
4
votes
4
replies
2.6k
views
Unexpected MAplot after apeglm shrinkage in DESeq2
apeglm deseq2 rna-seq
updated 6.6 years ago by 43k • written 6.6 years ago by ★ 4.8k
4
votes
2
replies
3.1k
views
Interpreting the results from lfcShrink() with apeglm in DESeq2
deseq2 apeglm lfcshrink
updated 6.6 years ago by 43k • written 6.6 years ago by ▴ 180
1
vote
4
replies
2.0k
views
Log2 fold-change shrinkage fails with lfcShrink when using the 'apeglm' method
deseq2 apeglm lfcshrink
6.8 years ago coulsonr ▴ 20
0
votes
4
replies
1.6k
views
Error in Apeglm Method for Effect Size Shrinkage
deseq2 apeglm
updated 6.9 years ago by 43k • written 6.9 years ago by ▴ 50
10
votes
6
replies
7.1k
views
Log2FoldChange shrinkage method in DESeq2
deseq2 apeglm lfcshrink
updated 7.0 years ago by 43k • written 7.0 years ago by ▴ 90
42 results • Page 1 of 1
Recent ...
Replies
Comment: DiffBind - question on the use of filtered or unfiltered input data by sloperun3az • 0
Your essay was beneficial to me, and I found it to be very useful. Thank you for writing it. You give a wealth of knowledge that is not onl…
Comment: compute_fasta_digest does not match Salmon index hash by sloperun3az • 0
The people who are reading your work are not taken into consideration, even though you appear to have a solid understanding of the subject …
Comment: parameters of filterByExpr by Paul Harrison ▴ 110
It might be worth trying limma-voom (or limma-trend) instead of a GLM based method. In our experience these are less prone to this problem.…
Comment: limma::voom vs edgeR::voomLmFit - when to use? by Gordon Smyth 52k
voomLmFit() is in edgeR instead of limma because it needs to call edgeR::glmFit() internally to determine which of the zero observations al…
Comment: limma::voom vs edgeR::voomLmFit - when to use? by Geoff • 0
Just wondering--why was this function put into `edgeR` rather than `limma`? Maybe a bit technical, but it is a little confusing from an out…
Votes
Comment: Check removeBatchEffect effectiveness
Answer: Check removeBatchEffect effectiveness
A: what should I do with many zero counts from Salmon quantification
Comment: parameters of filterByExpr
GAlignments Cigar to GRanges
Awards • All
Scholar to James W. MacDonald 68k
Popular Question to Gordon Smyth 52k
Scholar to Hervé Pagès 16k
Popular Question to Bine ▴ 50
Popular Question to RobKo ▴ 10
Locations • All
United States, 51 minutes ago
Australia, 1 hour ago
United States, 1 hour ago
United States, 1 hour ago
Indonesia, 1 hour ago
Traffic: 492 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