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Showing :
ApeGLM
•
reset
1
vote
2
replies
333
views
Questions in Regards to LFC shrinkage in DESeq2
Dseq2
RNASeqData
apeglm
3 months ago
Gordon
• 0
2
votes
10
replies
896
views
How to run allelic imbalance in apeglm
apeglm
7 months ago • updated 6 months ago
euge.eugenio
▴ 20
0
votes
1
reply
840
views
lfcShrink error: the line search routine failed
apeglm
DESeq2
updated 9 months ago by
Michael Love
43k • written 9 months ago by
Yuqin
• 0
0
votes
2
replies
1.5k
views
Error: insufficient numeric precision during Log fold change shrinkage with apeglm
apeglm
updated 15 months ago by
Michael Love
43k • written 16 months ago by
Juan Pablo
• 0
0
votes
4
replies
945
views
lfc direction of effect flipped for ashr, apeGLM, but accurate to biological data for non-shrunken
DESeq2
apeglm
DESeq
ApeGLM
Ashr
updated 17 months ago by
Michael Love
43k • written 17 months ago by
Ndimensional
▴ 20
2
votes
7
replies
2.4k
views
optimHess problem in apeglm/DESeq2
DESeq2
apeglm
updated 19 months ago by
Michael Love
43k • written 19 months ago by
ATpoint
★ 4.6k
3
votes
2
replies
1.2k
views
DESeq2 lfcShrink: swapping reference gives different results for the same comparison
DESeq2
apeglm
21 months ago • updated 20 months ago
Daphnia
• 0
1
vote
5
replies
2.4k
views
DESeq2 outlier options and LFC Shrinkage
DESeq2
RNASeq
RnaSeqSampleSize
apeglm
updated 2.4 years ago by
Michael Love
43k • written 2.4 years ago by
Riley
• 0
1
vote
3
replies
1.2k
views
LFC shrinkage setting negative LFC svalues to zero
DESeq2
DifferentialExpression
apeglm
updated 2.4 years ago by
Michael Love
43k • written 2.4 years ago by
81das_col
• 0
1
vote
2
replies
1.1k
views
running apeglm on a normal model and multiple coefficients
shrinkage
apeglm
2.7 years ago
Frederik Ziebell
▴ 30
1
vote
2
replies
1.5k
views
Use of shrunken LFCs to address questions about the distribution of LFCs between gene categories.
deseq2
apeglm
DESeq2
2.9 years ago
i.sudbery
▴ 40
2
votes
3
replies
2.2k
views
Choosing an svalue threshold from apeglm shrunken results in DESeq2
apeglm
DESeq2
updated 3.3 years ago by
Michael Love
43k • written 3.3 years ago by
i.sudbery
▴ 40
1
vote
5
replies
1.8k
views
lfcShrink probelm in many 0 count genes RNA-seq data
ashr
DESeq2
apeglm
updated 3.3 years ago by
Michael Love
43k • written 3.4 years ago by
Guandong Shang
▴ 40
0
votes
1
reply
867
views
Non-significant but high LFC after apeglm shrinkage
DESeq2
apeglm
updated 3.8 years ago by
Michael Love
43k • written 3.8 years ago by
hpapoli
• 0
0
votes
1
reply
1.3k
views
Plotting the most expressed genes after conducting DESeq2
DESeq2
pheatmap
apeglm
updated 3.9 years ago by
Michael Love
43k • written 3.9 years ago by
amoaristotle
▴ 10
2
votes
2
replies
1.4k
views
DESeq2 in R
DESeq2
apeglm
updated 3.9 years ago by
swbarnes2
★ 1.4k • written 3.9 years ago by
amoaristotle
▴ 10
0
votes
2
replies
1.5k
views
DSEQ apeglm
DESeq2
apeglm
3.9 years ago
amoaristotle
▴ 10
2
votes
1
reply
1.4k
views
apeglm -- influence of reference level on logFC and svalues
DESeq2
apeglm
updated 3.9 years ago by
Michael Love
43k • written 3.9 years ago by
ATpoint
★ 4.6k
0
votes
3
replies
1.2k
views
Using altHypothesis on apleglm-shrunken log2FoldChanges
apeglm
DESeq2
4.0 years ago
zefrieira
• 0
0
votes
1
reply
1.2k
views
DESeq2 - shrunken LFC calculation
apeglm
DESeq2
updated 4.0 years ago by
Michael Love
43k • written 4.0 years ago by
alexandr.gopanenko
▴ 50
0
votes
3
replies
839
views
Influence of DEG in ASE analysis within apeglm
apeglm
updated 4.2 years ago by
Michael Love
43k • written 4.2 years ago by
Vincent.C.
• 0
1
vote
1
reply
791
views
Exceeding Over-dispersion parameter bbEstDisp
apeglm
bbEstdisp
allele ratio
updated 4.3 years ago by
Michael Love
43k • written 4.3 years ago by
Vincent.C.
• 0
5
votes
10
replies
1.6k
views
Allelic imbalance in apeglm
apeglm
Allelic imbalance
concept
updated 4.3 years ago by
Michael Love
43k • written 4.3 years ago by
Vincent.C.
• 0
1
vote
4
replies
2.1k
views
Using different LFC shrinkage estimators for spike-in normalised RNA-seq data
deseq2
apeglm
rna-seq
spike-in
updated 4.4 years ago by
Michael Love
43k • written 4.4 years ago by
nadezda.fursova
▴ 10
3
votes
2
replies
2.4k
views
lfcShrink function in DEseq2 and s-values
deseq2
apeglm
updated 4.4 years ago by
Michael Love
43k • written 4.4 years ago by
josmantorres
▴ 10
2
votes
1
reply
843
views
What are the steps to use a complex model of Allelic imbalance through apeglm
apeglm
complex model
ASE
Allelic imbalance
updated 4.4 years ago by
Michael Love
43k • written 4.4 years ago by
Vincent.C.
• 0
1
vote
1
reply
1.0k
views
Why s-values instead of p-values with non-default lfcThreshold and apeglm shrinkage in DESeq2
deseq2
apeglm
updated 4.5 years ago by
Michael Love
43k • written 4.5 years ago by
jabaron.phd
• 0
3
votes
4
replies
2.5k
views
Reporting S values? Reporting padj values?
deseq2
apeglm
updated 4.6 years ago by
Michael Love
43k • written 4.6 years ago by
n.tear
▴ 20
4
votes
4
replies
3.1k
views
RNA seq analysis using Deseq2 and apeglm lfc shrinkage
deseq2
fdrtool
apeglm
updated 4.7 years ago by
Michael Love
43k • written 4.7 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 5.0 years ago by
Michael Love
43k • written 5.0 years ago by
coulsonr
▴ 20
0
votes
2
replies
1.5k
views
lfcShrink in DESeq2
deseq2
apeglm
updated 5.4 years ago by
Michael Love
43k • written 5.4 years ago by
Meghdad
• 0
3
votes
3
replies
1.7k
views
Using alternative LFC shrinkage methods for computing p-values in DESeq2
deseq2
apeglm
statistics
updated 5.6 years ago by
Michael Love
43k • written 5.6 years ago by
zefrieira
• 0
3
votes
2
replies
1.8k
views
Calculate S/N ratios from apeglm for GSEA
apeglm
fgsea
Signal-To-Noise Ratio
updated 5.6 years ago by
Michael Love
43k • written 5.6 years ago by
coulsonr
▴ 20
2
votes
1
reply
1.1k
views
Deactivate svalue=T in lfcShrink - DESeq2 - apeglm
deseq2
apeglm
updated 5.7 years ago by
Michael Love
43k • written 5.7 years ago by
ATpoint
★ 4.6k
2
votes
4
replies
1.5k
views
What is the biological meaning of genes with FC = 0 after shrinkage
deseq2
apeglm
updated 5.8 years ago by
Michael Love
43k • written 5.8 years ago by
polyptwo
• 0
0
votes
2
replies
3.1k
views
DESeq2 coefficients for APEGLM-shrinkage
deseq2
apeglm
updated 6.1 years ago by
Michael Love
43k • written 6.1 years ago by
zolotaryovgl
• 0
4
votes
4
replies
2.4k
views
Unexpected MAplot after apeglm shrinkage in DESeq2
apeglm
deseq2
rna-seq
updated 6.2 years ago by
Michael Love
43k • written 6.2 years ago by
ATpoint
★ 4.6k
4
votes
2
replies
2.9k
views
Interpreting the results from lfcShrink() with apeglm in DESeq2
deseq2
apeglm
lfcshrink
updated 6.2 years ago by
Michael Love
43k • written 6.2 years ago by
charles.foster
▴ 160
1
vote
4
replies
1.9k
views
Log2 fold-change shrinkage fails with lfcShrink when using the 'apeglm' method
deseq2
apeglm
lfcshrink
6.4 years ago
coulsonr
▴ 20
0
votes
4
replies
1.4k
views
Error in Apeglm Method for Effect Size Shrinkage
deseq2
apeglm
updated 6.5 years ago by
Michael Love
43k • written 6.5 years ago by
rbenel
▴ 40
10
votes
6
replies
6.4k
views
Log2FoldChange shrinkage method in DESeq2
deseq2
apeglm
lfcshrink
updated 6.6 years ago by
Michael Love
43k • written 6.6 years ago by
Benjamin Ostendorf
▴ 90
41 results • Page
1 of 1
Recent ...
Replies
Comment: Cross-validation with multiple control subgroups in limma
by
Ali Barry
▴ 40
Thanks so much for taking the time here, the insights are much appreciated. I suspected I'd have to ad hoc compare results if I did repeat …
Answer: Cross-validation with multiple control subgroups in limma
by
Gordon Smyth
52k
limma doesn't do cross-validation or resampling. Like most classical linear modeling procedures in statistics, limma uses a statistical mod…
Comment: Issues with seqlevelsStyle when making custom txdb objects for genomes/annotatio
by
Robert Castelo
★ 3.4k
Hi Hervé, thank you very much for your input into how to properly build and manage TxDb objects. gDNAx has two main inputs, one or more BAM…
Comment: Biostrings: Error writing long reads (>200 kbps) with writeQualityScaledXStringS
by
Aidan
▴ 60
Quick update: this is fixed in a branch awaiting PR to Biostrings (https://github.com/Bioconductor/Biostrings/pull/122). Should be in `deve…
Answer: Can DESeq2's design compensate for sequencing experimental design shortcomings?
by
Michael Love
43k
For statistical analysis plans, I recommend working with a local statistician or someone familiar with linear models in R. I have to reserv…
Votes
Comment: Issues with seqlevelsStyle when making custom txdb objects for genomes/annotatio
C: edgeR and lack of counts ID on CPM matrix
A: DESeq2 Following RSEM
A: importing RSEM data into DESeq2
A: Expected counts from RSEM in DESeq2
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