Showing : apeglm • reset
0
Votes
3
Replies
88
Views
Using altHypothesis on apleglm-shrunken log2FoldChanges
apeglm DESeq2
12 days ago zefrieira • 0
0
Votes
1
Reply
64
Views
DESeq2 - shrunken LFC calculation
apeglm DESeq2
16 days ago alexandr.gopanenko • 20 • updated 16 days ago Michael Love 31k
0
Votes
3
Replies
70
Views
Influence of DEG in ASE analysis within apeglm
apeglm
3 months ago Vincent.C. • 0 • updated 3 months ago Michael Love 31k
1
Vote
1
Reply
69
Views
Exceeding Over-dispersion parameter bbEstDisp
apeglm bbEstdisp allele ratio
4 months ago Vincent.C. • 0 • updated 4 months ago Michael Love 31k
5
Votes
10
Replies
138
Views
Allelic imbalance in apeglm
apeglm Allelic imbalance concept
5 months ago Vincent.C. • 0 • updated 5 months ago Michael Love 31k
0
Votes
4
Replies
184
Views
Using different LFC shrinkage estimators for spike-in normalised RNA-seq data
deseq2 apeglm rna-seq spike-in
5 months ago nadezda.fursova • 0 • updated 5 months ago Michael Love 31k
2
Votes
2
Replies
118
Views
lfcShrink function in DEseq2 and s-values
deseq2 apeglm
5 months ago josmantorres • 10 • updated 5 months ago Michael Love 31k
2
Votes
1
Reply
80
Views
What are the steps to use a complex model of Allelic imbalance through apeglm
apeglm complex model ASE Allelic imbalance
5 months ago Vincent.C. • 0 • updated 5 months ago Michael Love 31k
1
Vote
1
Reply
76
Views
Why s-values instead of p-values with non-default lfcThreshold and apeglm shrinkage in DESeq2
deseq2 apeglm
7 months ago jabaron.phd • 0 • updated 7 months ago Michael Love 31k
0
Votes
4
Replies
176
Views
Reporting S values? Reporting padj values?
deseq2 apeglm
7 months ago n.tear • 10 • updated 7 months ago Michael Love 31k
4
Votes
4
Replies
103
Views
RNA seq analysis using Deseq2 and apeglm lfc shrinkage
deseq2 fdrtool apeglm
9 months ago Paul • 0 • updated 9 months ago Michael Love 31k
0
Votes
2
Replies
137
Views
Coefficient names for multiple group comparisons to use with lfcShrink & apeglm
deseq2 lfcShrink apeglm
13 months ago coulsonr • 10 • updated 13 months ago Michael Love 31k
0
Votes
2
Replies
355
Views
lfcShrink in DESeq2
deseq2 apeglm
17 months ago Meghdad • 0 • updated 17 months ago Michael Love 31k
3
Votes
3
Replies
252
Views
Using alternative LFC shrinkage methods for computing p-values in DESeq2
deseq2 apeglm statistics
20 months ago zefrieira • 0 • updated 20 months ago Michael Love 31k
0
Votes
2
Replies
194
Views
Calculate S/N ratios from apeglm for GSEA
apeglm fgsea Signal-To-Noise Ratio
20 months ago coulsonr • 10 • updated 20 months ago Michael Love 31k
2
Votes
1
Reply
248
Views
Deactivate svalue=T in lfcShrink - DESeq2 - apeglm
deseq2 apeglm
21 months ago ATpoint • 390 • updated 21 months ago Michael Love 31k
2
Votes
4
Replies
360
Views
What is the biological meaning of genes with FC = 0 after shrinkage
deseq2 apeglm
22 months ago polyptwo • 0 • updated 22 months ago Michael Love 31k
0
Votes
2
Replies
917
Views
DESeq2 coefficients for APEGLM-shrinkage
deseq2 apeglm
2.2 years ago zolotaryovgl • 0 • updated 2.2 years ago Michael Love 31k
4
Votes
4
Replies
754
Views
Unexpected MAplot after apeglm shrinkage in DESeq2
apeglm deseq2 rna-seq
2.2 years ago ATpoint • 390 • updated 2.2 years ago Michael Love 31k
4
Votes
2
Replies
917
Views
Interpreting the results from lfcShrink() with apeglm in DESeq2
deseq2 apeglm lfcshrink
2.3 years ago charles.foster • 100 • updated 2.3 years ago Michael Love 31k
1
Vote
4
Replies
631
Views
Log2 fold-change shrinkage fails with lfcShrink when using the 'apeglm' method
deseq2 apeglm lfcshrink
2.5 years ago coulsonr • 10
0
Votes
4
Replies
306
Views
Error in Apeglm Method for Effect Size Shrinkage
deseq2 apeglm
2.6 years ago rbenel • 10 • updated 2.6 years ago Michael Love 31k
9
Votes
6
Replies
1.7k
Views
Log2FoldChange shrinkage method in DESeq2
deseq2 apeglm lfcshrink
2.7 years ago Benjamin Ostendorf • 90 • updated 2.7 years ago Michael Love 31k
23 results • Page 1 of 1
Recent ...
Replies
Answer: The compare result is different in score and Conc in DiffBind by shangguandong1996 • 20
I know in newer DiffBind version, the default of `score` argument is different, So I post a newer DiffBind version result. ``` library(…
Answer: Conc_1 in differnet dba.report result is slightly different by shangguandong1996 • 20
For a newer DiffBind version ``` library(DiffBind) library(BiocParallel) library(dplyr) tamoxifen <- dba(sampleSheet="tamoxifen.csv") ta…
Comment: Conc_1 in differnet dba.report result is slightly different by shangguandong1996 • 20
Hi, Dr Stark I just find you fixed the link, and I want to use the test data to reproduce my issue ``` library(DiffBind) library(BiocPara…
Comment: DESeq2 and shrinkage of log2 fold changes by Asier • 0
One question related to this. In the case of using the schrinkage (in my dataset of miRNA-seq) the number of SDE miRNAs (FDR) increases wit…
Comment: [Limma] Correcting Dye swap effect by MatthewP • 0
Hello, Can you explain "M vs M plot" with more details? I have include dye-effect in limma design model, and got very few probes differenti…
Votes
A: Performing differential gene analysis on RT PCR experimental data
A: Performing differential gene analysis on RT PCR experimental data
Comment: DESeq2: Significant padj and LFC in a 0 vs. 20 counts comparison?
A: Using the plotting functions of clusterProfiler / enrichplot with enrichment res
Comment: DESeq2: Significant padj and LFC in a 0 vs. 20 counts comparison?
Awards • All
Popular Question to wewolski • 10
Popular Question to efratsh • 0
Prophet to ilysR • 0
Popular Question to Sophie Marion de Proce • 0
Prophet to jol.espinoz • 30
Locations • All
America, 15 minutes ago
WEHI, Melbourne, Australia, 23 minutes ago
Switzerland, 33 minutes ago
Germany, 44 minutes ago
Zurich, 1 hour ago
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 2.3.3