Showing : ApeGLM • reset
1
vote
4
replies
1.6k
views
Log2 fold-change shrinkage fails with lfcShrink when using the 'apeglm' method
deseq2 apeglm lfcshrink
5.8 years ago coulsonr ▴ 20
0
votes
2
replies
879
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
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
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 ★ 4.1k
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
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
2
votes
1
reply
980
views
Deactivate svalue=T in lfcShrink - DESeq2 - apeglm
deseq2 apeglm
updated 5.1 years ago by 42k • written 5.1 years ago by ★ 4.1k
3
votes
2
replies
1.4k
views
Calculate S/N ratios from apeglm for GSEA
apeglm fgsea Signal-To-Noise Ratio
updated 5.0 years ago by 42k • written 5.0 years ago by ▴ 20
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
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
0
votes
2
replies
950
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
4
votes
4
replies
2.5k
views
RNA seq analysis using Deseq2 and apeglm lfc shrinkage
deseq2 fdrtool apeglm
updated 4.1 years ago by 42k • written 4.1 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
1
vote
1
reply
811
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
2
votes
1
reply
679
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
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
5
votes
10
replies
1.3k
views
Allelic imbalance in apeglm
apeglm Allelic imbalance concept
updated 3.7 years ago by 42k • written 3.7 years ago by • 0
1
vote
1
reply
631
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
3
replies
671
views
Influence of DEG in ASE analysis within apeglm
apeglm
updated 3.6 years ago by 42k • written 3.6 years ago by • 0
0
votes
1
reply
958
views
DESeq2 - shrunken LFC calculation
apeglm DESeq2
updated 3.4 years ago by 42k • written 3.4 years ago by ▴ 50
0
votes
3
replies
1.0k
views
Using altHypothesis on apleglm-shrunken log2FoldChanges
apeglm DESeq2
3.4 years ago zefrieira • 0
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 ★ 4.1k
0
votes
2
replies
1.3k
views
DSEQ apeglm
DESeq2 apeglm
3.3 years ago amoaristotle ▴ 10
0
votes
1
reply
995
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
0
votes
1
reply
711
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
3
votes
2
replies
822
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
2
replies
1.2k
views
Use of shrunken LFCs to address questions about the distribution of LFCs between gene categories.
deseq2 apeglm DESeq2
2.3 years ago i.sudbery ▴ 40
1
vote
5
replies
1.9k
views
DESeq2 outlier options and LFC Shrinkage
DESeq2 RNASeq RnaSeqSampleSize apeglm
updated 21 months ago by 42k • written 21 months ago by • 0
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 ★ 4.1k
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
0
votes
2
replies
849
views
running apeglm on a normal model and multiple coefficients
shrinkage apeglm
2.1 years ago Frederik Ziebell ▴ 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
0
votes
4
replies
673
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
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
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
1
reply
214
views
lfcShrink error: the line search routine failed
apeglm DESeq2
updated 8 weeks ago by 42k • written 8 weeks ago by • 0
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
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
39 results • Page 1 of 1
Recent ...
Replies
Answer: Subsetting RNAseq data | voomaByGroup() by Gordon Smyth 50k
Judging from your MDS plot, cell types 1 and 2 look radically different, so it would make perfect sense to analyse them separately. There's…
Answer: Numerical differences in DESeq2 output depending on different design matrix cons by Michael Love 42k
Yes there can be small numerical differences in the estimated quantities because of how the algorithms decide to stop iterating.
Answer: DESeq2- Mysterious interaction suppresses DEGs by Michael Love 42k
Removing samples from one group nevertheless changes the variance estimation (dispersion) for all comparisons. So you could have pushed one…
Comment: Ensembl plants at annotationHub? by Daniele • 0
Hi, I'm using Ensembl Plants release 59 with the IWGSC RefSeq v1.1 gene annotation. Thanks a lot for replying so quickly!
Comment: Numerical differences in DESeq2 output depending on different design matrix cons by swbarnes2 ★ 1.4k
If you restrict yourself to, say, genes with a baseMean > 50, are the numerical differences between the two designs significant?
Votes
Answer: Error while installing BiocManager::install("org.Vdahliae.eg.db")
Comment: How can I create a eigencorplot of pca created from deseq2 object with PCAtools
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
Rsubread counting peaks ATACseq
Awards • All
Popular Question to Dario Strbenac ★ 1.5k
Popular Question to Vincent J. Carey, Jr. 6.7k
Popular Question to Koen Van den Berge ▴ 180
Popular Question to shepherl 3.9k
Popular Question to Ken C • 0
Locations • All
WEHI, Melbourne, Australia, 3 minutes ago
Australia, 41 minutes ago
Melbourne, Australia, 53 minutes ago
United States, 59 minutes ago
UPF, Barcelona, Spain, 2 hours ago
Traffic: 266 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