Showing : ApeGLM • reset
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Questions in Regards to LFC shrinkage in DESeq2
Dseq2 RNASeqData apeglm
6 months ago Gordon • 0
2
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10
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1.0k
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How to run allelic imbalance in apeglm
apeglm
9 months ago • updated 8 months ago euge.eugenio ▴ 20
0
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1
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1.1k
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lfcShrink error: the line search routine failed
apeglm DESeq2
updated 11 months ago by 43k • written 11 months ago by • 0
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2
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1.6k
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Error: insufficient numeric precision during Log fold change shrinkage with apeglm
apeglm
updated 18 months ago by 43k • written 18 months ago by • 0
0
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4
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1.0k
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lfc direction of effect flipped for ashr, apeGLM, but accurate to biological data for non-shrunken
DESeq2 apeglm DESeq ApeGLM Ashr
updated 19 months ago by 43k • written 19 months ago by ▴ 20
2
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7
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2.6k
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optimHess problem in apeglm/DESeq2
DESeq2 apeglm
updated 22 months ago by 43k • written 22 months ago by ★ 4.7k
3
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2
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1.2k
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DESeq2 lfcShrink: swapping reference gives different results for the same comparison
DESeq2 apeglm
23 months ago Daphnia • 0
1
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5
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2.6k
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DESeq2 outlier options and LFC Shrinkage
DESeq2 RNASeq RnaSeqSampleSize apeglm
updated 2.6 years ago by 43k • written 2.6 years ago by • 0
1
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3
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1.3k
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LFC shrinkage setting negative LFC svalues to zero
DESeq2 DifferentialExpression apeglm
updated 2.6 years ago by 43k • written 2.6 years ago by • 0
1
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2
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1.2k
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running apeglm on a normal model and multiple coefficients
shrinkage apeglm
2.9 years ago Frederik Ziebell ▴ 30
1
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2
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1.5k
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Use of shrunken LFCs to address questions about the distribution of LFCs between gene categories.
deseq2 apeglm DESeq2
3.1 years ago i.sudbery ▴ 40
2
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3
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2.3k
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Choosing an svalue threshold from apeglm shrunken results in DESeq2
apeglm DESeq2
updated 3.5 years ago by 43k • written 3.5 years ago by ▴ 40
1
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5
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1.9k
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lfcShrink probelm in many 0 count genes RNA-seq data
ashr DESeq2 apeglm
updated 3.5 years ago by 43k • written 3.6 years ago by ▴ 40
0
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1
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901
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Non-significant but high LFC after apeglm shrinkage
DESeq2 apeglm
updated 4.0 years ago by 43k • written 4.0 years ago by • 0
0
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1
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1.4k
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Plotting the most expressed genes after conducting DESeq2
DESeq2 pheatmap apeglm
updated 4.1 years ago by 43k • written 4.1 years ago by ▴ 10
2
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2
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1.4k
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DESeq2 in R
DESeq2 apeglm
updated 4.1 years ago by ★ 1.4k • written 4.1 years ago by ▴ 10
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2
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1.5k
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DSEQ apeglm
DESeq2 apeglm
4.1 years ago amoaristotle ▴ 10
2
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1
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1.5k
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apeglm -- influence of reference level on logFC and svalues
DESeq2 apeglm
updated 4.1 years ago by 43k • written 4.1 years ago by ★ 4.7k
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3
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1.2k
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Using altHypothesis on apleglm-shrunken log2FoldChanges
apeglm DESeq2
4.1 years ago zefrieira • 0
0
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1
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1.3k
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DESeq2 - shrunken LFC calculation
apeglm DESeq2
updated 4.2 years ago by 43k • written 4.2 years ago by ▴ 50
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3
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892
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Influence of DEG in ASE analysis within apeglm
apeglm
updated 4.4 years ago by 43k • written 4.4 years ago by • 0
1
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1
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835
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Exceeding Over-dispersion parameter bbEstDisp
apeglm bbEstdisp allele ratio
updated 4.5 years ago by 43k • written 4.5 years ago by • 0
5
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10
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1.7k
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Allelic imbalance in apeglm
apeglm Allelic imbalance concept
updated 4.5 years ago by 43k • written 4.5 years ago by • 0
1
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4
replies
2.2k
views
Using different LFC shrinkage estimators for spike-in normalised RNA-seq data
deseq2 apeglm rna-seq spike-in
updated 4.6 years ago by 43k • written 4.6 years ago by ▴ 10
3
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2
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2.5k
views
lfcShrink function in DEseq2 and s-values
deseq2 apeglm
updated 4.6 years ago by 43k • written 4.6 years ago by ▴ 10
2
votes
1
reply
891
views
What are the steps to use a complex model of Allelic imbalance through apeglm
apeglm complex model ASE Allelic imbalance
updated 4.6 years ago by 43k • written 4.6 years ago by • 0
1
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1
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1.1k
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Why s-values instead of p-values with non-default lfcThreshold and apeglm shrinkage in DESeq2
deseq2 apeglm
updated 4.7 years ago by 43k • written 4.7 years ago by • 0
3
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4
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2.6k
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Reporting S values? Reporting padj values?
deseq2 apeglm
updated 4.7 years ago by 43k • written 4.7 years ago by ▴ 20
4
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4
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3.3k
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RNA seq analysis using Deseq2 and apeglm lfc shrinkage
deseq2 fdrtool apeglm
updated 4.9 years ago by 43k • written 4.9 years ago by • 0
0
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2
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1.2k
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Coefficient names for multiple group comparisons to use with lfcShrink & apeglm
deseq2 lfcShrink apeglm
updated 5.2 years ago by 43k • written 5.2 years ago by ▴ 20
0
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2
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1.5k
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lfcShrink in DESeq2
deseq2 apeglm
updated 5.6 years ago by 43k • written 5.6 years ago by • 0
3
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3
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1.8k
views
Using alternative LFC shrinkage methods for computing p-values in DESeq2
deseq2 apeglm statistics
updated 5.8 years ago by 43k • written 5.8 years ago by • 0
3
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2
replies
1.9k
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Calculate S/N ratios from apeglm for GSEA
apeglm fgsea Signal-To-Noise Ratio
updated 5.8 years ago by 43k • written 5.8 years ago by ▴ 20
2
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1
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1.2k
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Deactivate svalue=T in lfcShrink - DESeq2 - apeglm
deseq2 apeglm
updated 5.9 years ago by 43k • written 5.9 years ago by ★ 4.7k
2
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4
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1.6k
views
What is the biological meaning of genes with FC = 0 after shrinkage
deseq2 apeglm
updated 6.0 years ago by 43k • written 6.0 years ago by • 0
0
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2
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3.2k
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DESeq2 coefficients for APEGLM-shrinkage
deseq2 apeglm
updated 6.3 years ago by 43k • written 6.3 years ago by • 0
4
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4
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2.5k
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Unexpected MAplot after apeglm shrinkage in DESeq2
apeglm deseq2 rna-seq
updated 6.4 years ago by 43k • written 6.4 years ago by ★ 4.7k
4
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2
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3.0k
views
Interpreting the results from lfcShrink() with apeglm in DESeq2
deseq2 apeglm lfcshrink
updated 6.4 years ago by 43k • written 6.4 years ago by ▴ 160
1
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4
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1.9k
views
Log2 fold-change shrinkage fails with lfcShrink when using the 'apeglm' method
deseq2 apeglm lfcshrink
6.6 years ago coulsonr ▴ 20
0
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4
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1.5k
views
Error in Apeglm Method for Effect Size Shrinkage
deseq2 apeglm
updated 6.7 years ago by 43k • written 6.7 years ago by ▴ 40
10
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6
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6.7k
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Log2FoldChange shrinkage method in DESeq2
deseq2 apeglm lfcshrink
updated 6.8 years ago by 43k • written 6.8 years ago by ▴ 90
41 results • Page 1 of 1
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Comment: how many significant figures are there in DESeq2 output by ATpoint ★ 4.7k
If you want consistency then use a fixed software environment like Docker, wirh fixed code and thresholds that make sense. Rounding to near…
Comment: Compare TCGA-PAAD with GTEx gene expression by Jane • 0
why aren't there any answers?
Comment: Too many significant genes when integrating gtex and tcga by Jane • 0
I encountered the same issue: too many DEGs after limma analysis. It is sad that until today we can still see the paper published where GTE…
Comment: how many significant figures are there in DESeq2 output by Matthew McCormack ▴ 180
Thank you for your reply. It is good to know that cutoff of 0.05 means less than 0.05. My concerns are about consistency and reproducibili…
Comment: DiffBind edgeR normalization --- why are the normalization factors all equal to by ATpoint ★ 4.7k
No, normalization factors from edgeR rather than size factors from DESeq2 are not proportional, it's a different concept and implementation…
Votes
A: Unbalanced experiment with multiple samples from each patient.
Unbalanced experiment with multiple samples from each patient.
Answer: Vertical line at A=0, nothing else, on MA plot
Answer: GSVA Error Code "Calling gsva(expr=., gset.idx.list=., method=., ...) is defunct
Answer: Group-specific condition effects with individuals nested: matrix is not full ra
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