Log In
Sign Up
about
faq
Ask a question
Latest
News
Jobs
Tutorials
Tags
Users
New Post
Latest
News
Jobs
Tutorials
Tags
Users
Log In
Sign Up
About
Limit
all time
today
this week
this month
this year
Unanswered
All posts
Sort
Update
Answers
Bookmarks
Creation
Replies
Rank
Views
Votes
Showing :
apeglm
•
reset
0
votes
2
replies
1.0k
views
Install old version of DESeq2
apeglm
Install
DESeq2
version
updated 16 days ago by
Kevin Blighe
★ 4.0k • written 5 months ago by
Asma
• 0
0
votes
1
reply
691
views
Which of apeglm and ashr may be more appropriate for pseudobulked DESeq2 analysis of single-cell RNA-seq data?
apeglm
DESeq2
updated 3 months ago by
Michael Love
43k • written 3 months ago by
KS
• 0
0
votes
4
replies
880
views
Using shrunken LFC and s-value from DESeq2 as DGE results
apeglm
s-value
DESeq2
updated 4 months ago by
Michael Love
43k • written 4 months ago by
Erika
• 0
3
votes
1
reply
649
views
DESeq2 Apeglm Coefficient Reordering / Log2FoldChange Comparison Change
DESeq2
apeglm
updated 6 months ago by
James W. MacDonald
68k • written 6 months ago by
sk
• 0
1
vote
2
replies
690
views
Questions in Regards to LFC shrinkage in DESeq2
Dseq2
RNASeqData
apeglm
15 months ago
Gordon
• 0
2
votes
10
replies
1.6k
views
How to run allelic imbalance in apeglm
apeglm
18 months ago
euge.eugenio
▴ 20
0
votes
1
reply
1.6k
views
lfcShrink error: the line search routine failed
apeglm
DESeq2
updated 21 months ago by
Michael Love
43k • written 21 months ago by
Yuqin
• 0
0
votes
2
replies
2.0k
views
Error: insufficient numeric precision during Log fold change shrinkage with apeglm
apeglm
updated 2.3 years ago by
Michael Love
43k • written 2.3 years ago by
Juan Pablo
• 0
0
votes
4
replies
1.4k
views
lfc direction of effect flipped for ashr, apeGLM, but accurate to biological data for non-shrunken
DESeq2
apeglm
DESeq
ApeGLM
Ashr
updated 2.4 years ago by
Michael Love
43k • written 2.4 years ago by
Ndimensional
▴ 20
2
votes
7
replies
3.0k
views
optimHess problem in apeglm/DESeq2
DESeq2
apeglm
updated 2.6 years ago by
Michael Love
43k • written 2.6 years ago by
ATpoint
★ 5.0k
3
votes
2
replies
1.5k
views
DESeq2 lfcShrink: swapping reference gives different results for the same comparison
DESeq2
apeglm
2.7 years ago
Daphnia
• 0
1
vote
5
replies
3.2k
views
DESeq2 outlier options and LFC Shrinkage
DESeq2
RNASeq
RnaSeqSampleSize
apeglm
updated 3.3 years ago by
Michael Love
43k • written 3.4 years ago by
Riley
• 0
1
vote
3
replies
1.6k
views
LFC shrinkage setting negative LFC svalues to zero
DESeq2
DifferentialExpression
apeglm
updated 3.4 years ago by
Michael Love
43k • written 3.4 years ago by
81das_col
• 0
1
vote
2
replies
1.5k
views
running apeglm on a normal model and multiple coefficients
shrinkage
apeglm
3.6 years ago
Frederik Ziebell
▴ 30
1
vote
2
replies
1.8k
views
Use of shrunken LFCs to address questions about the distribution of LFCs between gene categories.
deseq2
apeglm
DESeq2
3.9 years ago
i.sudbery
▴ 40
2
votes
3
replies
2.7k
views
Choosing an svalue threshold from apeglm shrunken results in DESeq2
apeglm
DESeq2
updated 4.2 years ago by
Michael Love
43k • written 4.3 years ago by
i.sudbery
▴ 40
1
vote
5
replies
2.3k
views
lfcShrink probelm in many 0 count genes RNA-seq data
ashr
DESeq2
apeglm
updated 4.3 years ago by
Michael Love
43k • written 4.3 years ago by
Guandong Shang
▴ 40
0
votes
1
reply
1.1k
views
Non-significant but high LFC after apeglm shrinkage
DESeq2
apeglm
updated 4.7 years ago by
Michael Love
43k • written 4.7 years ago by
hpapoli
• 0
0
votes
1
reply
1.7k
views
Plotting the most expressed genes after conducting DESeq2
DESeq2
pheatmap
apeglm
updated 4.8 years ago by
Michael Love
43k • written 4.8 years ago by
amoaristotle
▴ 10
2
votes
2
replies
1.6k
views
DESeq2 in R
DESeq2
apeglm
updated 4.8 years ago by
swbarnes2
★ 1.4k • written 4.8 years ago by
amoaristotle
▴ 10
0
votes
2
replies
1.7k
views
DSEQ apeglm
DESeq2
apeglm
4.8 years ago
amoaristotle
▴ 10
2
votes
1
reply
1.8k
views
apeglm -- influence of reference level on logFC and svalues
DESeq2
apeglm
updated 4.8 years ago by
Michael Love
43k • written 4.8 years ago by
ATpoint
★ 5.0k
0
votes
3
replies
1.5k
views
Using altHypothesis on apleglm-shrunken log2FoldChanges
apeglm
DESeq2
4.9 years ago
zefrieira
• 0
0
votes
1
reply
1.5k
views
DESeq2 - shrunken LFC calculation
apeglm
DESeq2
updated 4.9 years ago by
Michael Love
43k • written 4.9 years ago by
alexandr.gopanenko
▴ 50
0
votes
3
replies
1.1k
views
Influence of DEG in ASE analysis within apeglm
apeglm
updated 5.2 years ago by
Michael Love
43k • written 5.2 years ago by
Vincent.C.
• 0
1
vote
1
reply
1.0k
views
Exceeding Over-dispersion parameter bbEstDisp
apeglm
bbEstdisp
allele ratio
updated 5.3 years ago by
Michael Love
43k • written 5.3 years ago by
Vincent.C.
• 0
5
votes
10
replies
2.1k
views
Allelic imbalance in apeglm
apeglm
Allelic imbalance
concept
updated 5.3 years ago by
Michael Love
43k • written 5.3 years ago by
Vincent.C.
• 0
1
vote
4
replies
2.6k
views
Using different LFC shrinkage estimators for spike-in normalised RNA-seq data
deseq2
apeglm
rna-seq
spike-in
updated 5.3 years ago by
Michael Love
43k • written 5.3 years ago by
nadezda.fursova
▴ 10
3
votes
2
replies
2.9k
views
lfcShrink function in DEseq2 and s-values
deseq2
apeglm
updated 5.3 years ago by
Michael Love
43k • written 5.3 years ago by
josmantorres
▴ 10
2
votes
1
reply
1.1k
views
What are the steps to use a complex model of Allelic imbalance through apeglm
apeglm
complex model
ASE
Allelic imbalance
updated 5.4 years ago by
Michael Love
43k • written 5.4 years ago by
Vincent.C.
• 0
1
vote
1
reply
1.3k
views
Why s-values instead of p-values with non-default lfcThreshold and apeglm shrinkage in DESeq2
deseq2
apeglm
updated 5.5 years ago by
Michael Love
43k • written 5.5 years ago by
jabaron.phd
• 0
3
votes
4
replies
3.0k
views
Reporting S values? Reporting padj values?
deseq2
apeglm
updated 5.5 years ago by
Michael Love
43k • written 5.5 years ago by
n.tear
▴ 20
4
votes
4
replies
4.0k
views
RNA seq analysis using Deseq2 and apeglm lfc shrinkage
deseq2
fdrtool
apeglm
updated 5.7 years ago by
Michael Love
43k • written 5.7 years ago by
Paul
• 0
0
votes
2
replies
1.4k
views
Coefficient names for multiple group comparisons to use with lfcShrink & apeglm
deseq2
lfcShrink
apeglm
updated 6.0 years ago by
Michael Love
43k • written 6.0 years ago by
coulsonr
▴ 20
0
votes
2
replies
1.8k
views
lfcShrink in DESeq2
deseq2
apeglm
updated 6.3 years ago by
Michael Love
43k • written 6.3 years ago by
Meghdad
• 0
3
votes
3
replies
2.1k
views
Using alternative LFC shrinkage methods for computing p-values in DESeq2
deseq2
apeglm
statistics
updated 6.5 years ago by
Michael Love
43k • written 6.5 years ago by
zefrieira
• 0
3
votes
2
replies
2.2k
views
Calculate S/N ratios from apeglm for GSEA
apeglm
fgsea
Signal-To-Noise Ratio
updated 6.6 years ago by
Michael Love
43k • written 6.6 years ago by
coulsonr
▴ 20
2
votes
1
reply
1.4k
views
Deactivate svalue=T in lfcShrink - DESeq2 - apeglm
deseq2
apeglm
updated 6.7 years ago by
Michael Love
43k • written 6.7 years ago by
ATpoint
★ 5.0k
2
votes
4
replies
2.0k
views
What is the biological meaning of genes with FC = 0 after shrinkage
deseq2
apeglm
updated 6.7 years ago by
Michael Love
43k • written 6.7 years ago by
polyptwo
• 0
0
votes
2
replies
3.6k
views
DESeq2 coefficients for APEGLM-shrinkage
deseq2
apeglm
updated 7.0 years ago by
Michael Love
43k • written 7.0 years ago by
zolotaryovgl
• 0
4
votes
4
replies
2.8k
views
Unexpected MAplot after apeglm shrinkage in DESeq2
apeglm
deseq2
rna-seq
updated 7.1 years ago by
Michael Love
43k • written 7.1 years ago by
ATpoint
★ 5.0k
4
votes
2
replies
3.4k
views
Interpreting the results from lfcShrink() with apeglm in DESeq2
deseq2
apeglm
lfcshrink
updated 7.2 years ago by
Michael Love
43k • written 7.2 years ago by
charles.foster
▴ 180
1
vote
4
replies
2.2k
views
Log2 fold-change shrinkage fails with lfcShrink when using the 'apeglm' method
deseq2
apeglm
lfcshrink
7.4 years ago • updated 7.3 years ago
coulsonr
▴ 20
0
votes
4
replies
1.8k
views
Error in Apeglm Method for Effect Size Shrinkage
deseq2
apeglm
updated 7.4 years ago by
Michael Love
43k • written 7.4 years ago by
rbenel
▴ 50
10
votes
6
replies
7.6k
views
Log2FoldChange shrinkage method in DESeq2
deseq2
apeglm
lfcshrink
updated 7.5 years ago by
Michael Love
43k • written 7.5 years ago by
Benjamin Ostendorf
▴ 90
45 results • Page
1 of 1
Recent ...
Replies
Comment: DECIPHER DesignProbes unable to design FISH-probes
by
Erik Wright
▴ 150
Are the sequences aligned (i.e., the same width) before running `TileSeqs()`?
Comment: BiocParallel (and DESeq2) - wrong args for environment subassignment
by
Michael Love
43k
BTW, I tested with no issue on MacOS ARM on our previous github issue.
Answer: DESeq(dds, parallel=TRUE) wrong args for environment subassignment
by
Michael Love
43k
The DESeq2 error makes sense, as we've talked about, given that the simple `bplapply` isn't working in your setup. Maybe give the traceb…
Answer: PTM analysis in LIMPA
by
Gordon Smyth
53k
For PTM analysis, the usual quantification command dpcQuant() is replaced by dpcImpute(). Otherwise the limpa pipeline is the same as for a…
Answer: problem reading bam files into nucleR
by
James W. MacDonald
68k
The first step is to update to the current versions of R/Bioconductor and try again. It's possible that you have run into a bug that's alre…
Votes
C: DESeq2 Following RSEM
Upcoming Ensembl API and data access changes - new blog post available
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
Answer: Large logFC but somewhat high FDR
Comment: upstream git branches of bioc-release
Awards
• All
Popular Question
to
Gordon Smyth
53k
Commentator
to
sina.nassiri
▴ 130
Popular Question
to
Hervé Pagès
16k
Popular Question
to
jared.andrews07
▴ 30
Popular Question
to
James W. MacDonald
68k
Locations
• All
Greece,
12 minutes ago
The city by the bay,
29 minutes ago
WEHI, Melbourne, Australia,
2 hours ago
United States,
3 hours ago
United States,
3 hours ago
Traffic: 1196 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