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ApeGLM
•
reset
1
vote
2
replies
475
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
11 months ago • updated 10 months ago
euge.eugenio
▴ 20
0
votes
1
reply
1.2k
views
lfcShrink error: the line search routine failed
apeglm
DESeq2
updated 13 months ago by
Michael Love
43k • written 13 months ago by
Yuqin
• 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
Michael Love
43k • written 20 months ago by
Juan Pablo
• 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 21 months ago by
Michael Love
43k • written 21 months ago by
Ndimensional
▴ 20
2
votes
7
replies
2.7k
views
optimHess problem in apeglm/DESeq2
DESeq2
apeglm
updated 23 months ago by
Michael Love
43k • written 23 months ago by
ATpoint
★ 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
2.7k
views
DESeq2 outlier options and LFC Shrinkage
DESeq2
RNASeq
RnaSeqSampleSize
apeglm
updated 2.7 years ago by
Michael Love
43k • written 2.7 years ago by
Riley
• 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
Michael Love
43k • written 2.8 years ago by
81das_col
• 0
1
vote
2
replies
1.3k
views
running apeglm on a normal model and multiple coefficients
shrinkage
apeglm
3.0 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
2.3k
views
Choosing an svalue threshold from apeglm shrunken results in DESeq2
apeglm
DESeq2
updated 3.6 years ago by
Michael Love
43k • written 3.6 years ago by
i.sudbery
▴ 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
Michael Love
43k • written 3.7 years ago by
Guandong Shang
▴ 40
0
votes
1
reply
927
views
Non-significant but high LFC after apeglm shrinkage
DESeq2
apeglm
updated 4.1 years ago by
Michael Love
43k • written 4.1 years ago by
hpapoli
• 0
0
votes
1
reply
1.5k
views
Plotting the most expressed genes after conducting DESeq2
DESeq2
pheatmap
apeglm
updated 4.2 years ago by
Michael Love
43k • written 4.2 years ago by
amoaristotle
▴ 10
2
votes
2
replies
1.4k
views
DESeq2 in R
DESeq2
apeglm
updated 4.2 years ago by
swbarnes2
★ 1.4k • written 4.2 years ago by
amoaristotle
▴ 10
0
votes
2
replies
1.5k
views
DSEQ apeglm
DESeq2
apeglm
4.2 years ago
amoaristotle
▴ 10
2
votes
1
reply
1.6k
views
apeglm -- influence of reference level on logFC and svalues
DESeq2
apeglm
updated 4.2 years ago by
Michael Love
43k • written 4.2 years ago by
ATpoint
★ 4.8k
0
votes
3
replies
1.3k
views
Using altHypothesis on apleglm-shrunken log2FoldChanges
apeglm
DESeq2
4.3 years ago
zefrieira
• 0
0
votes
1
reply
1.3k
views
DESeq2 - shrunken LFC calculation
apeglm
DESeq2
updated 4.3 years ago by
Michael Love
43k • written 4.3 years ago by
alexandr.gopanenko
▴ 50
0
votes
3
replies
921
views
Influence of DEG in ASE analysis within apeglm
apeglm
updated 4.6 years ago by
Michael Love
43k • written 4.6 years ago by
Vincent.C.
• 0
1
vote
1
reply
863
views
Exceeding Over-dispersion parameter bbEstDisp
apeglm
bbEstdisp
allele ratio
updated 4.6 years ago by
Michael Love
43k • written 4.6 years ago by
Vincent.C.
• 0
5
votes
10
replies
1.8k
views
Allelic imbalance in apeglm
apeglm
Allelic imbalance
concept
updated 4.7 years ago by
Michael Love
43k • written 4.7 years ago by
Vincent.C.
• 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 4.7 years ago by
Michael Love
43k • written 4.7 years ago by
nadezda.fursova
▴ 10
3
votes
2
replies
2.6k
views
lfcShrink function in DEseq2 and s-values
deseq2
apeglm
updated 4.7 years ago by
Michael Love
43k • written 4.7 years ago by
josmantorres
▴ 10
2
votes
1
reply
938
views
What are the steps to use a complex model of Allelic imbalance through apeglm
apeglm
complex model
ASE
Allelic imbalance
updated 4.7 years ago by
Michael Love
43k • written 4.7 years ago by
Vincent.C.
• 0
1
vote
1
reply
1.1k
views
Why s-values instead of p-values with non-default lfcThreshold and apeglm shrinkage in DESeq2
deseq2
apeglm
updated 4.8 years ago by
Michael Love
43k • written 4.8 years ago by
jabaron.phd
• 0
3
votes
4
replies
2.7k
views
Reporting S values? Reporting padj values?
deseq2
apeglm
updated 4.9 years ago by
Michael Love
43k • written 4.9 years ago by
n.tear
▴ 20
4
votes
4
replies
3.5k
views
RNA seq analysis using Deseq2 and apeglm lfc shrinkage
deseq2
fdrtool
apeglm
updated 5.1 years ago by
Michael Love
43k • written 5.1 years ago by
Paul
• 0
0
votes
2
replies
1.2k
views
Coefficient names for multiple group comparisons to use with lfcShrink & apeglm
deseq2
lfcShrink
apeglm
updated 5.4 years ago by
Michael Love
43k • written 5.4 years ago by
coulsonr
▴ 20
0
votes
2
replies
1.6k
views
lfcShrink in DESeq2
deseq2
apeglm
updated 5.7 years ago by
Michael Love
43k • written 5.7 years ago by
Meghdad
• 0
3
votes
3
replies
1.9k
views
Using alternative LFC shrinkage methods for computing p-values in DESeq2
deseq2
apeglm
statistics
updated 5.9 years ago by
Michael Love
43k • written 5.9 years ago by
zefrieira
• 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
Michael Love
43k • written 6.0 years ago by
coulsonr
▴ 20
2
votes
1
reply
1.2k
views
Deactivate svalue=T in lfcShrink - DESeq2 - apeglm
deseq2
apeglm
updated 6.0 years ago by
Michael Love
43k • written 6.0 years ago by
ATpoint
★ 4.8k
2
votes
4
replies
1.7k
views
What is the biological meaning of genes with FC = 0 after shrinkage
deseq2
apeglm
updated 6.1 years ago by
Michael Love
43k • written 6.1 years ago by
polyptwo
• 0
0
votes
2
replies
3.3k
views
DESeq2 coefficients for APEGLM-shrinkage
deseq2
apeglm
updated 6.4 years ago by
Michael Love
43k • written 6.4 years ago by
zolotaryovgl
• 0
4
votes
4
replies
2.6k
views
Unexpected MAplot after apeglm shrinkage in DESeq2
apeglm
deseq2
rna-seq
updated 6.5 years ago by
Michael Love
43k • written 6.5 years ago by
ATpoint
★ 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
Michael Love
43k • written 6.6 years ago by
charles.foster
▴ 180
1
vote
4
replies
2.0k
views
Log2 fold-change shrinkage fails with lfcShrink when using the 'apeglm' method
deseq2
apeglm
lfcshrink
6.7 years ago
coulsonr
▴ 20
0
votes
4
replies
1.5k
views
Error in Apeglm Method for Effect Size Shrinkage
deseq2
apeglm
updated 6.8 years ago by
Michael Love
43k • written 6.8 years ago by
rbenel
▴ 40
10
votes
6
replies
7.0k
views
Log2FoldChange shrinkage method in DESeq2
deseq2
apeglm
lfcshrink
updated 6.9 years ago by
Michael Love
43k • written 6.9 years ago by
Benjamin Ostendorf
▴ 90
41 results • Page
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Comment: GSEA preranked analysis downstream of DEseq2
by
Ajay
• 0
`logFC * -log10(pval)` seems to be the pi-score proposed in this [paper][1] [1]: https://pmc.ncbi.nlm.nih.gov/articles/PMC3957066/
Comment: error in ChAMP loading file
by
janwilseo
• 0
Any update on this post? I also had an issue with this. [erosion control](https://charlestonhydroseeding.com/)
Answer: CluserProfiler message "No gene can be mapped"
by
James W. MacDonald
68k
Two things. First, the order of your term2gene is backwards (should be term and then gene, like the name), and by default `enricher` adjust…
Comment: Controlling for batch and estrus cycle using DESeq2 in RNA-seq analysis
by
donnycrimson
• 0
One potential workaround might be to adjust for these factors using a combination of design matrices perhaps including batch as a covariate…
Comment: DESeq2 Design controlling for gender
by
donnycrimson
• 0
On a lighter note, while you are tackling such complex data, you might enjoy a quick break playing the [Slope Game](https://slopegame.lol)…
Votes
DiffBind; Error: No sites have activity greater than filter value
remove X and Y chromosome genes in RNA-seq data using DESeq2 pipeline
How to remove X & Y chromosome genes from RNAseq data
Is it advisable to remove X and Y chromosome genes in mouse bulk RNA-seq data at the level of the count matrix?
A: Unbalanced experiment with multiple samples from each patient.
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