Showing : apeglm • reset
0
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158
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lfcShrink error: the line search routine failed
apeglm DESeq2
updated 4 weeks ago by 41k • written 4 weeks ago by • 0
0
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2
replies
775
views
Error: insufficient numeric precision during Log fold change shrinkage with apeglm
apeglm
updated 7 months ago by 41k • written 8 months ago by • 0
0
votes
4
replies
616
views
lfc direction of effect flipped for ashr, apeGLM, but accurate to biological data for non-shrunken
DESeq2 apeglm DESeq ApeGLM Ashr
updated 9 months ago by 41k • written 9 months ago by ▴ 20
2
votes
7
replies
1.8k
views
optimHess problem in apeglm/DESeq2
DESeq2 apeglm
updated 11 months ago by 41k • written 11 months ago by ★ 4.0k
3
votes
2
replies
769
views
DESeq2 lfcShrink: swapping reference gives different results for the same comparison
DESeq2 apeglm
13 months ago • updated 12 months ago Daphnia • 0
1
vote
5
replies
1.8k
views
DESeq2 outlier options and LFC Shrinkage
DESeq2 RNASeq RnaSeqSampleSize apeglm
updated 20 months ago by 41k • written 20 months ago by • 0
1
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3
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957
views
LFC shrinkage setting negative LFC svalues to zero
DESeq2 DifferentialExpression apeglm
updated 21 months ago by 41k • written 21 months ago by • 0
0
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2
replies
814
views
running apeglm on a normal model and multiple coefficients
shrinkage apeglm
24 months ago Frederik Ziebell ▴ 20
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 ▴ 30
1
vote
3
replies
1.6k
views
Choosing an svalue threshold from apeglm shrunken results in DESeq2
apeglm DESeq2
updated 2.6 years ago by 41k • written 2.6 years ago by ▴ 30
1
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5
replies
1.4k
views
lfcShrink probelm in many 0 count genes RNA-seq data
ashr DESeq2 apeglm
updated 2.6 years ago by 41k • written 2.7 years ago by ▴ 40
0
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1
reply
689
views
Non-significant but high LFC after apeglm shrinkage
DESeq2 apeglm
updated 3.1 years ago by 41k • written 3.1 years ago by • 0
0
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1
reply
950
views
Plotting the most expressed genes after conducting DESeq2
DESeq2 pheatmap apeglm
updated 3.2 years ago by 41k • written 3.2 years ago by ▴ 10
2
votes
2
replies
1.1k
views
DESeq2 in R
DESeq2 apeglm
updated 3.2 years ago by ★ 1.3k • written 3.2 years ago by ▴ 10
0
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2
replies
1.2k
views
DSEQ apeglm
DESeq2 apeglm
3.2 years ago amoaristotle ▴ 10
2
votes
1
reply
1.1k
views
apeglm -- influence of reference level on logFC and svalues
DESeq2 apeglm
updated 3.2 years ago by 41k • written 3.2 years ago by ★ 4.0k
0
votes
3
replies
989
views
Using altHypothesis on apleglm-shrunken log2FoldChanges
apeglm DESeq2
3.3 years ago zefrieira • 0
0
votes
1
reply
922
views
DESeq2 - shrunken LFC calculation
apeglm DESeq2
updated 3.3 years ago by 41k • written 3.3 years ago by ▴ 50
0
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3
replies
654
views
Influence of DEG in ASE analysis within apeglm
apeglm
updated 3.5 years ago by 41k • written 3.5 years ago by • 0
1
vote
1
reply
619
views
Exceeding Over-dispersion parameter bbEstDisp
apeglm bbEstdisp allele ratio
updated 3.6 years ago by 41k • written 3.6 years ago by • 0
5
votes
10
replies
1.2k
views
Allelic imbalance in apeglm
apeglm Allelic imbalance concept
updated 3.6 years ago by 41k • written 3.7 years ago by • 0
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 3.7 years ago by 41k • written 3.7 years ago by ▴ 10
3
votes
2
replies
1.8k
views
lfcShrink function in DEseq2 and s-values
deseq2 apeglm
updated 3.7 years ago by 41k • written 3.7 years ago by ▴ 10
2
votes
1
reply
658
views
What are the steps to use a complex model of Allelic imbalance through apeglm
apeglm complex model ASE Allelic imbalance
updated 3.7 years ago by 41k • written 3.7 years ago by • 0
1
vote
1
reply
786
views
Why s-values instead of p-values with non-default lfcThreshold and apeglm shrinkage in DESeq2
deseq2 apeglm
updated 3.8 years ago by 41k • written 3.8 years ago by • 0
3
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4
replies
2.1k
views
Reporting S values? Reporting padj values?
deseq2 apeglm
updated 3.9 years ago by 41k • written 3.9 years ago by ▴ 20
4
votes
4
replies
2.5k
views
RNA seq analysis using Deseq2 and apeglm lfc shrinkage
deseq2 fdrtool apeglm
updated 4.0 years ago by 41k • written 4.0 years ago by • 0
0
votes
2
replies
925
views
Coefficient names for multiple group comparisons to use with lfcShrink & apeglm
deseq2 lfcShrink apeglm
updated 4.3 years ago by 41k • written 4.3 years ago by ▴ 20
0
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2
replies
1.2k
views
lfcShrink in DESeq2
deseq2 apeglm
updated 4.7 years ago by 41k • written 4.7 years ago by • 0
3
votes
3
replies
1.4k
views
Using alternative LFC shrinkage methods for computing p-values in DESeq2
deseq2 apeglm statistics
updated 4.9 years ago by 41k • written 4.9 years ago by • 0
3
votes
2
replies
1.4k
views
Calculate S/N ratios from apeglm for GSEA
apeglm fgsea Signal-To-Noise Ratio
updated 4.9 years ago by 41k • written 4.9 years ago by ▴ 20
2
votes
1
reply
959
views
Deactivate svalue=T in lfcShrink - DESeq2 - apeglm
deseq2 apeglm
updated 5.0 years ago by 41k • written 5.0 years ago by ★ 4.0k
2
votes
4
replies
1.3k
views
What is the biological meaning of genes with FC = 0 after shrinkage
deseq2 apeglm
updated 5.1 years ago by 41k • written 5.1 years ago by • 0
0
votes
2
replies
2.6k
views
DESeq2 coefficients for APEGLM-shrinkage
deseq2 apeglm
updated 5.4 years ago by 41k • written 5.4 years ago by • 0
4
votes
4
replies
2.1k
views
Unexpected MAplot after apeglm shrinkage in DESeq2
apeglm deseq2 rna-seq
updated 5.5 years ago by 41k • written 5.5 years ago by ★ 4.0k
4
votes
2
replies
2.5k
views
Interpreting the results from lfcShrink() with apeglm in DESeq2
deseq2 apeglm lfcshrink
updated 5.5 years ago by 41k • written 5.5 years ago by ▴ 160
1
vote
4
replies
1.6k
views
Log2 fold-change shrinkage fails with lfcShrink when using the 'apeglm' method
deseq2 apeglm lfcshrink
5.7 years ago coulsonr ▴ 20
0
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4
replies
1.1k
views
Error in Apeglm Method for Effect Size Shrinkage
deseq2 apeglm
updated 5.8 years ago by 41k • written 5.8 years ago by ▴ 40
10
votes
6
replies
5.2k
views
Log2FoldChange shrinkage method in DESeq2
deseq2 apeglm lfcshrink
updated 5.9 years ago by 41k • written 5.9 years ago by ▴ 90
39 results • Page 1 of 1
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Comment: Theoretical WGCNA Question by Garrett • 0
Thanks Peter!
Comment: FGSEA pre-ranked input in increasing order or decreasing by sropri • 0
Thank you!
Comment: FGSEA pre-ranked input in increasing order or decreasing by alserg ▴ 240
They are reorder in the decreasing order.
Comment: significant difference of p-values with dream() after updating VariancePartition by Le • 0
Thanks for your reply @gabrielhoffman ! I've been trying to isolate the changes, and v1.32.5 had the same results as v1.33.1 while v1.30.0…
Comment: How to tell and visualize up/down regulation of pathways from clusterprofiler gs by sredemption • 0
Try library(enrichplot) dotplot(gsea_FS, showCategory=10, split=".sign") + facet_grid(.~.sign)
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How to tell and visualize up/down regulation of pathways from clusterprofiler gsea output
Comment: DEXSeq DEXSeqDataSet count matrix duplication
Comment: Error in champ.load(): The following specified files do not exist
Answer: Error in read.metharray(basenames = files, extended = extended, verbose = verbos
Using GRanges and IRanges to simply get all chromosome data
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