Showing : ApeGLM • reset
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
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
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
2.6k
views
RNA seq analysis using Deseq2 and apeglm lfc shrinkage
deseq2 fdrtool apeglm
updated 4.2 years ago by 42k • written 4.2 years ago by • 0
3
votes
4
replies
2.2k
views
Reporting S values? Reporting padj values?
deseq2 apeglm
updated 4.0 years ago by 42k • written 4.0 years ago by ▴ 20
4
votes
4
replies
2.1k
views
Unexpected MAplot after apeglm shrinkage in DESeq2
apeglm deseq2 rna-seq
updated 5.6 years ago by 42k • written 5.6 years ago by ★ 4.2k
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 ★ 4.2k
1
vote
5
replies
1.9k
views
DESeq2 outlier options and LFC Shrinkage
DESeq2 RNASeq RnaSeqSampleSize apeglm
updated 22 months ago by 42k • written 22 months ago by • 0
3
votes
2
replies
1.9k
views
lfcShrink function in DEseq2 and s-values
deseq2 apeglm
updated 3.8 years ago by 42k • written 3.8 years ago by ▴ 10
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 3.8 years ago by 42k • written 3.8 years ago by ▴ 10
1
vote
4
replies
1.7k
views
Log2 fold-change shrinkage fails with lfcShrink when using the 'apeglm' method
deseq2 apeglm lfcshrink
5.8 years ago coulsonr ▴ 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
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 2.8 years ago by ▴ 40
3
votes
3
replies
1.4k
views
Using alternative LFC shrinkage methods for computing p-values in DESeq2
deseq2 apeglm statistics
updated 5.0 years ago by 42k • written 5.0 years ago by • 0
3
votes
2
replies
1.4k
views
Calculate S/N ratios from apeglm for GSEA
apeglm fgsea Signal-To-Noise Ratio
updated 5.1 years ago by 42k • written 5.1 years ago by ▴ 20
2
votes
4
replies
1.3k
views
What is the biological meaning of genes with FC = 0 after shrinkage
deseq2 apeglm
updated 5.2 years ago by 42k • written 5.2 years ago by • 0
0
votes
2
replies
1.3k
views
DSEQ apeglm
DESeq2 apeglm
3.3 years ago amoaristotle ▴ 10
5
votes
10
replies
1.3k
views
Allelic imbalance in apeglm
apeglm Allelic imbalance concept
updated 3.8 years ago by 42k • written 3.8 years ago by • 0
0
votes
2
replies
1.3k
views
lfcShrink in DESeq2
deseq2 apeglm
updated 4.8 years ago by 42k • written 4.8 years 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
2.4 years ago i.sudbery ▴ 40
0
votes
4
replies
1.2k
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
2
votes
2
replies
1.2k
views
DESeq2 in R
DESeq2 apeglm
updated 3.3 years ago by ★ 1.4k • written 3.3 years ago by ▴ 10
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 ★ 4.2k
0
votes
3
replies
1.0k
views
Using altHypothesis on apleglm-shrunken log2FoldChanges
apeglm DESeq2
3.4 years ago zefrieira • 0
1
vote
3
replies
1.0k
views
LFC shrinkage setting negative LFC svalues to zero
DESeq2 DifferentialExpression apeglm
updated 22 months ago by 42k • written 22 months ago by • 0
0
votes
1
reply
1.0k
views
Plotting the most expressed genes after conducting DESeq2
DESeq2 pheatmap apeglm
updated 3.3 years ago by 42k • written 3.3 years ago by ▴ 10
2
votes
1
reply
982
views
Deactivate svalue=T in lfcShrink - DESeq2 - apeglm
deseq2 apeglm
updated 5.1 years ago by 42k • written 5.1 years ago by ★ 4.2k
0
votes
1
reply
964
views
DESeq2 - shrunken LFC calculation
apeglm DESeq2
updated 3.4 years ago by 42k • written 3.4 years ago by ▴ 50
0
votes
2
replies
956
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
2
replies
898
views
Error: insufficient numeric precision during Log fold change shrinkage with apeglm
apeglm
updated 8 months ago by 42k • written 9 months ago by • 0
0
votes
2
replies
857
views
running apeglm on a normal model and multiple coefficients
shrinkage apeglm
2.1 years ago Frederik Ziebell ▴ 20
3
votes
2
replies
839
views
DESeq2 lfcShrink: swapping reference gives different results for the same comparison
DESeq2 apeglm
14 months ago • updated 13 months ago Daphnia • 0
1
vote
1
reply
823
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
0
votes
1
reply
714
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
2
votes
1
reply
686
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
0
votes
4
replies
683
views
lfc direction of effect flipped for ashr, apeGLM, but accurate to biological data for non-shrunken
DESeq2 apeglm DESeq ApeGLM Ashr
updated 10 months ago by 42k • written 10 months ago by ▴ 20
0
votes
3
replies
674
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
1
reply
636
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
229
views
lfcShrink error: the line search routine failed
apeglm DESeq2
updated 9 weeks ago by 42k • written 10 weeks ago by • 0
1
vote
2
replies
106
views
How to run allelic imbalance in apeglm
apeglm
updated 6 days ago by 42k • written 7 days ago by ▴ 20
40 results • Page 1 of 1
Recent ...
Replies
Comment: How to add Ensembl ids after Pseudobulk analysis by DESeq2 by BioinfGuru ▴ 30
I would use biomaRt. This is what happens when annotation occurs to early. If possible I would run the DEG analysis on the original output…
Comment: Volcano plot of scRNA-seq data not "centered" by ATpoint ★ 4.2k
My comment was generic. If your experiment causes drastic shifts then the situation might be different. The advise is the same: Try to use …
Comment: conumee with Infinium MethylationEPIC v2.0 by Maximus • 0
Hi Sole, If there is a combined mixture of MSet of 450K, EPIC and EPICv2, how should I create an annotation object? I tried to create anno…
Comment: Volcano plot of scRNA-seq data not "centered" by tjl • 0
Thank you both. The code is below, simplified a bit for simplicity. ATpoint, your suggestion re: the top 20% of genes by baseMean makes me …
Comment: Cannot install oligo on Fedora by James W. MacDonald 66k
Wait a minute. The `oligo` package is *supposed to* be using `zlibbioc`, but apparently it is not. I get the same thing as you do, where it…
Votes
A: Analyzing data without replicates using DiffBind
A: Analyzing data without replicates using DiffBind
DeSeq2 results converting ENSG IDs to Gene Symbols, more than one ENSG ID per Gene symbol
DESeq2 swap ensembl gene id rownames with gene symbol column
A: DeSeq2 results converting ENSG IDs to Gene Symbols, more than one ENSG ID per Ge
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