Showing : apeglm • reset
0
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167
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lfcShrink error: the line search routine failed
apeglm DESeq2
updated 5 weeks ago by 41k • written 5 weeks ago by • 0
0
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2
replies
801
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
633
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
786
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 21 months ago by 41k • written 21 months ago by • 0
1
vote
3
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968
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
829
views
running apeglm on a normal model and multiple coefficients
shrinkage apeglm
2.0 years 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 ▴ 40
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 ▴ 40
1
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5
replies
1.4k
views
lfcShrink probelm in many 0 count genes RNA-seq data
ashr DESeq2 apeglm
updated 2.7 years ago by 41k • written 2.7 years ago by ▴ 40
0
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1
reply
696
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
votes
1
reply
962
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
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3
replies
994
views
Using altHypothesis on apleglm-shrunken log2FoldChanges
apeglm DESeq2
3.3 years ago zefrieira • 0
0
votes
1
reply
935
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
663
views
Influence of DEG in ASE analysis within apeglm
apeglm
updated 3.6 years ago by 41k • written 3.6 years ago by • 0
1
vote
1
reply
626
views
Exceeding Over-dispersion parameter bbEstDisp
apeglm bbEstdisp allele ratio
updated 3.7 years ago by 41k • written 3.7 years ago by • 0
5
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10
replies
1.2k
views
Allelic imbalance in apeglm
apeglm Allelic imbalance concept
updated 3.7 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
665
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
794
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
votes
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 4.1 years ago by 41k • written 4.1 years ago by • 0
0
votes
2
replies
936
views
Coefficient names for multiple group comparisons to use with lfcShrink & apeglm
deseq2 lfcShrink apeglm
updated 4.4 years ago by 41k • written 4.4 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 5.0 years ago by 41k • written 5.0 years ago by ▴ 20
2
votes
1
reply
964
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
2.6k
views
Interpreting the results from lfcShrink() with apeglm in DESeq2
deseq2 apeglm lfcshrink
updated 5.6 years ago by 41k • written 5.6 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
votes
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
5.3k
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: Math expression in shapeCustom legend in EnhancedVolcano by pl23 • 0
Thank you very much - that worked perfectly! Word of warning to those who try this: it screws up the other legends because of the markdown …
Answer: PCA plot suggestions by Michael Love 41k
For help with interpretation and design of analysis, I recommend working with a local statistician. Due to time restrictions, I can only…
Comment: DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length by ussarizona ▴ 10
Hi Michael, Yes, I could figure it out what does the error mean. In my matrix I had the first colum GeneID while in my condition I only h…
Answer: Deseq2. decontXcounts not integers. Useful alternative? by Michael Love 41k
Another option would be to put the per sample estimated contamination in the design. This is for example how RUV etc help remove spurious D…
Answer: ATACseq merge peaks by ATpoint ★ 4.0k
That depends on your analysis. Typically, for differential analysis (and convenience) you would produce a single set of peaks (e.g. by merg…
Votes
Answer: Math expression in shapeCustom legend in EnhancedVolcano
Comment: DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
Comment: Deseq2. decontXcounts not integers. Useful alternative?
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2)
biomaRt error: database disk image is malformed
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