Showing : apeglm • reset
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Which of apeglm and ashr may be more appropriate for pseudobulked DESeq2 analysis of single-cell RNA-seq data?
apeglm DESeq2
6 days ago KS • 0
0
votes
4
replies
737
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Using shrunken LFC and s-value from DESeq2 as DGE results
apeglm s-value DESeq2
updated 28 days ago by 43k • written 6 weeks ago by • 0
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2
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865
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Install old version of DESeq2
apeglm Install DESeq2 version
updated 7 weeks ago by 68k • written 7 weeks ago by • 0
3
votes
1
reply
530
views
DESeq2 Apeglm Coefficient Reordering / Log2FoldChange Comparison Change
DESeq2 apeglm
updated 3 months ago by 68k • written 3 months ago by • 0
1
vote
2
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605
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Questions in Regards to LFC shrinkage in DESeq2
Dseq2 RNASeqData apeglm
12 months ago Gordon • 0
2
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10
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1.4k
views
How to run allelic imbalance in apeglm
apeglm
15 months ago • updated 14 months ago euge.eugenio ▴ 20
0
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1
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1.5k
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lfcShrink error: the line search routine failed
apeglm DESeq2
updated 17 months ago by 43k • written 17 months ago by • 0
0
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2
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1.9k
views
Error: insufficient numeric precision during Log fold change shrinkage with apeglm
apeglm
updated 2.0 years ago by 43k • written 2.0 years ago by • 0
0
votes
4
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1.3k
views
lfc direction of effect flipped for ashr, apeGLM, but accurate to biological data for non-shrunken
DESeq2 apeglm DESeq ApeGLM Ashr
updated 2.1 years ago by 43k • written 2.1 years ago by ▴ 20
2
votes
7
replies
2.9k
views
optimHess problem in apeglm/DESeq2
DESeq2 apeglm
updated 2.3 years ago by 43k • written 2.3 years ago by ★ 4.9k
3
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2
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1.4k
views
DESeq2 lfcShrink: swapping reference gives different results for the same comparison
DESeq2 apeglm
2.4 years ago Daphnia • 0
1
vote
5
replies
3.0k
views
DESeq2 outlier options and LFC Shrinkage
DESeq2 RNASeq RnaSeqSampleSize apeglm
updated 3.1 years ago by 43k • written 3.1 years ago by • 0
1
vote
3
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1.5k
views
LFC shrinkage setting negative LFC svalues to zero
DESeq2 DifferentialExpression apeglm
updated 3.1 years ago by 43k • written 3.1 years ago by • 0
1
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2
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1.4k
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running apeglm on a normal model and multiple coefficients
shrinkage apeglm
3.4 years ago • updated 3.3 years ago Frederik Ziebell ▴ 30
1
vote
2
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1.7k
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Use of shrunken LFCs to address questions about the distribution of LFCs between gene categories.
deseq2 apeglm DESeq2
3.6 years ago i.sudbery ▴ 40
2
votes
3
replies
2.5k
views
Choosing an svalue threshold from apeglm shrunken results in DESeq2
apeglm DESeq2
updated 4.0 years ago by 43k • written 4.0 years ago by ▴ 40
1
vote
5
replies
2.1k
views
lfcShrink probelm in many 0 count genes RNA-seq data
ashr DESeq2 apeglm
updated 4.0 years ago by 43k • written 4.0 years ago by ▴ 40
0
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1
reply
1.0k
views
Non-significant but high LFC after apeglm shrinkage
DESeq2 apeglm
updated 4.5 years ago by 43k • written 4.5 years ago by • 0
0
votes
1
reply
1.6k
views
Plotting the most expressed genes after conducting DESeq2
DESeq2 pheatmap apeglm
updated 4.6 years ago by 43k • written 4.6 years ago by ▴ 10
2
votes
2
replies
1.5k
views
DESeq2 in R
DESeq2 apeglm
updated 4.6 years ago by ★ 1.4k • written 4.6 years ago by ▴ 10
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2
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1.7k
views
DSEQ apeglm
DESeq2 apeglm
4.6 years ago amoaristotle ▴ 10
2
votes
1
reply
1.7k
views
apeglm -- influence of reference level on logFC and svalues
DESeq2 apeglm
updated 4.6 years ago by 43k • written 4.6 years ago by ★ 4.9k
0
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3
replies
1.4k
views
Using altHypothesis on apleglm-shrunken log2FoldChanges
apeglm DESeq2
4.6 years ago zefrieira • 0
0
votes
1
reply
1.4k
views
DESeq2 - shrunken LFC calculation
apeglm DESeq2
updated 4.7 years ago by 43k • written 4.7 years ago by ▴ 50
0
votes
3
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1.0k
views
Influence of DEG in ASE analysis within apeglm
apeglm
updated 4.9 years ago by 43k • written 4.9 years ago by • 0
1
vote
1
reply
939
views
Exceeding Over-dispersion parameter bbEstDisp
apeglm bbEstdisp allele ratio
updated 5.0 years ago by 43k • written 5.0 years ago by • 0
5
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10
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1.9k
views
Allelic imbalance in apeglm
apeglm Allelic imbalance concept
updated 5.0 years ago by 43k • written 5.0 years ago by • 0
1
vote
4
replies
2.4k
views
Using different LFC shrinkage estimators for spike-in normalised RNA-seq data
deseq2 apeglm rna-seq spike-in
updated 5.0 years ago by 43k • written 5.1 years ago by ▴ 10
3
votes
2
replies
2.8k
views
lfcShrink function in DEseq2 and s-values
deseq2 apeglm
updated 5.1 years ago by 43k • written 5.1 years ago by ▴ 10
2
votes
1
reply
1.0k
views
What are the steps to use a complex model of Allelic imbalance through apeglm
apeglm complex model ASE Allelic imbalance
updated 5.1 years ago by 43k • written 5.1 years ago by • 0
1
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1
reply
1.2k
views
Why s-values instead of p-values with non-default lfcThreshold and apeglm shrinkage in DESeq2
deseq2 apeglm
updated 5.2 years ago by 43k • written 5.2 years ago by • 0
3
votes
4
replies
2.9k
views
Reporting S values? Reporting padj values?
deseq2 apeglm
updated 5.2 years ago by 43k • written 5.2 years ago by ▴ 20
4
votes
4
replies
3.8k
views
RNA seq analysis using Deseq2 and apeglm lfc shrinkage
deseq2 fdrtool apeglm
updated 5.4 years ago by 43k • written 5.4 years ago by • 0
0
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2
replies
1.4k
views
Coefficient names for multiple group comparisons to use with lfcShrink & apeglm
deseq2 lfcShrink apeglm
updated 5.7 years ago by 43k • written 5.7 years ago by ▴ 20
0
votes
2
replies
1.7k
views
lfcShrink in DESeq2
deseq2 apeglm
updated 6.1 years ago by 43k • written 6.1 years ago by • 0
3
votes
3
replies
2.0k
views
Using alternative LFC shrinkage methods for computing p-values in DESeq2
deseq2 apeglm statistics
updated 6.3 years ago by 43k • written 6.3 years ago by • 0
3
votes
2
replies
2.1k
views
Calculate S/N ratios from apeglm for GSEA
apeglm fgsea Signal-To-Noise Ratio
updated 6.3 years ago by 43k • written 6.3 years ago by ▴ 20
2
votes
1
reply
1.3k
views
Deactivate svalue=T in lfcShrink - DESeq2 - apeglm
deseq2 apeglm
updated 6.4 years ago by 43k • written 6.4 years ago by ★ 4.9k
2
votes
4
replies
1.9k
views
What is the biological meaning of genes with FC = 0 after shrinkage
deseq2 apeglm
updated 6.5 years ago by 43k • written 6.5 years ago by • 0
0
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2
replies
3.5k
views
DESeq2 coefficients for APEGLM-shrinkage
deseq2 apeglm
updated 6.8 years ago by 43k • written 6.8 years ago by • 0
4
votes
4
replies
2.7k
views
Unexpected MAplot after apeglm shrinkage in DESeq2
apeglm deseq2 rna-seq
updated 6.9 years ago by 43k • written 6.9 years ago by ★ 4.9k
4
votes
2
replies
3.3k
views
Interpreting the results from lfcShrink() with apeglm in DESeq2
deseq2 apeglm lfcshrink
updated 6.9 years ago by 43k • written 6.9 years ago by ▴ 180
1
vote
4
replies
2.1k
views
Log2 fold-change shrinkage fails with lfcShrink when using the 'apeglm' method
deseq2 apeglm lfcshrink
7.1 years ago coulsonr ▴ 20
0
votes
4
replies
1.7k
views
Error in Apeglm Method for Effect Size Shrinkage
deseq2 apeglm
updated 7.2 years ago by 43k • written 7.2 years ago by ▴ 50
10
votes
6
replies
7.4k
views
Log2FoldChange shrinkage method in DESeq2
deseq2 apeglm lfcshrink
updated 7.3 years ago by 43k • written 7.3 years ago by ▴ 90
45 results • Page 1 of 1
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Replies
Comment: How to account for solvent controls in DESeq2 when comparing follicular vs lutea by snijesh ▴ 200
I would like to clarify whether the command `res <- results(dds, name = "phaseLP.conditionTreated")` is the correct approach to generate …
Comment: How to account for solvent controls in DESeq2 when comparing follicular vs lutea by James W. MacDonald 68k
Not sure I understand. You ask how to do something and then show how one would do so.
Comment: DiffBind getting Fold values of near 0 by littlefishes20 ▴ 10
Same issues. All peaks return to a fold near 0, although they are significant when visualizing in IGV. Please find the MAplot and volcanoPl…
Comment: How to account for solvent controls in DESeq2 when comparing follicular vs lutea by snijesh ▴ 200
I have checked DEGs between Solvent Control (SC) of FP and LP and there are noticebale differences in terms of DEGs. ``` # Checking SC in …
Answer: A0A287BB68 not recognized as UNPROT key in org.Ss.eg.db using AnnotationDbi::sel by James W. MacDonald 68k
Apparently it's been over-ridden by a different UniProtKB ID ``` > select(org.Ss.eg.db, "MYH11", "UNIPROT", "SYMBOL") 'select()' retu…
Votes
How to account for solvent controls in DESeq2 when comparing follicular vs luteal phase?
Answer: How to account for solvent controls in DESeq2 when comparing follicular vs lutea
Answer: How to account for solvent controls in DESeq2 when comparing follicular vs lutea
Comment: Using DESeq2 on single cell RNA Seq data of same cell type but different conditi
Can NanoString data be analyzed using DESeq2?
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