Showing : apeglm • reset
1
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Questions in Regards to LFC shrinkage in DESeq2
Dseq2 RNASeqData apeglm
8 months ago Gordon • 0
2
votes
10
replies
1.2k
views
How to run allelic imbalance in apeglm
apeglm
11 months ago • updated 10 months ago euge.eugenio ▴ 20
0
votes
1
reply
1.2k
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lfcShrink error: the line search routine failed
apeglm DESeq2
updated 13 months ago by 43k • written 13 months ago by • 0
0
votes
2
replies
1.8k
views
Error: insufficient numeric precision during Log fold change shrinkage with apeglm
apeglm
updated 20 months ago by 43k • written 20 months ago by • 0
0
votes
4
replies
1.1k
views
lfc direction of effect flipped for ashr, apeGLM, but accurate to biological data for non-shrunken
DESeq2 apeglm DESeq ApeGLM Ashr
updated 21 months ago by 43k • written 21 months ago by ▴ 20
2
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7
replies
2.7k
views
optimHess problem in apeglm/DESeq2
DESeq2 apeglm
updated 24 months ago by 43k • written 24 months ago by ★ 4.8k
3
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2
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1.3k
views
DESeq2 lfcShrink: swapping reference gives different results for the same comparison
DESeq2 apeglm
2.1 years ago Daphnia • 0
1
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5
replies
2.7k
views
DESeq2 outlier options and LFC Shrinkage
DESeq2 RNASeq RnaSeqSampleSize apeglm
updated 2.7 years ago by 43k • written 2.7 years ago by • 0
1
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3
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1.4k
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LFC shrinkage setting negative LFC svalues to zero
DESeq2 DifferentialExpression apeglm
updated 2.8 years ago by 43k • written 2.8 years ago by • 0
1
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2
replies
1.3k
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running apeglm on a normal model and multiple coefficients
shrinkage apeglm
3.0 years ago Frederik Ziebell ▴ 30
1
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2
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1.6k
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Use of shrunken LFCs to address questions about the distribution of LFCs between gene categories.
deseq2 apeglm DESeq2
3.3 years ago i.sudbery ▴ 40
2
votes
3
replies
2.3k
views
Choosing an svalue threshold from apeglm shrunken results in DESeq2
apeglm DESeq2
updated 3.6 years ago by 43k • written 3.7 years ago by ▴ 40
1
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5
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2.0k
views
lfcShrink probelm in many 0 count genes RNA-seq data
ashr DESeq2 apeglm
updated 3.7 years ago by 43k • written 3.7 years ago by ▴ 40
0
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1
reply
930
views
Non-significant but high LFC after apeglm shrinkage
DESeq2 apeglm
updated 4.1 years ago by 43k • written 4.1 years ago by • 0
0
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1
reply
1.5k
views
Plotting the most expressed genes after conducting DESeq2
DESeq2 pheatmap apeglm
updated 4.2 years ago by 43k • written 4.2 years ago by ▴ 10
2
votes
2
replies
1.5k
views
DESeq2 in R
DESeq2 apeglm
updated 4.2 years ago by ★ 1.4k • written 4.2 years ago by ▴ 10
0
votes
2
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1.5k
views
DSEQ apeglm
DESeq2 apeglm
4.2 years ago amoaristotle ▴ 10
2
votes
1
reply
1.6k
views
apeglm -- influence of reference level on logFC and svalues
DESeq2 apeglm
updated 4.2 years ago by 43k • written 4.2 years ago by ★ 4.8k
0
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3
replies
1.3k
views
Using altHypothesis on apleglm-shrunken log2FoldChanges
apeglm DESeq2
4.3 years ago zefrieira • 0
0
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1
reply
1.3k
views
DESeq2 - shrunken LFC calculation
apeglm DESeq2
updated 4.3 years ago by 43k • written 4.3 years ago by ▴ 50
0
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3
replies
922
views
Influence of DEG in ASE analysis within apeglm
apeglm
updated 4.6 years ago by 43k • written 4.6 years ago by • 0
1
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1
reply
869
views
Exceeding Over-dispersion parameter bbEstDisp
apeglm bbEstdisp allele ratio
updated 4.7 years ago by 43k • written 4.7 years ago by • 0
5
votes
10
replies
1.8k
views
Allelic imbalance in apeglm
apeglm Allelic imbalance concept
updated 4.7 years ago by 43k • written 4.7 years ago by • 0
1
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4
replies
2.3k
views
Using different LFC shrinkage estimators for spike-in normalised RNA-seq data
deseq2 apeglm rna-seq spike-in
updated 4.7 years ago by 43k • written 4.7 years ago by ▴ 10
3
votes
2
replies
2.7k
views
lfcShrink function in DEseq2 and s-values
deseq2 apeglm
updated 4.7 years ago by 43k • written 4.7 years ago by ▴ 10
2
votes
1
reply
942
views
What are the steps to use a complex model of Allelic imbalance through apeglm
apeglm complex model ASE Allelic imbalance
updated 4.8 years ago by 43k • written 4.8 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 4.9 years ago by 43k • written 4.9 years ago by • 0
3
votes
4
replies
2.7k
views
Reporting S values? Reporting padj values?
deseq2 apeglm
updated 4.9 years ago by 43k • written 4.9 years ago by ▴ 20
4
votes
4
replies
3.6k
views
RNA seq analysis using Deseq2 and apeglm lfc shrinkage
deseq2 fdrtool apeglm
updated 5.1 years ago by 43k • written 5.1 years ago by • 0
0
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2
replies
1.3k
views
Coefficient names for multiple group comparisons to use with lfcShrink & apeglm
deseq2 lfcShrink apeglm
updated 5.4 years ago by 43k • written 5.4 years ago by ▴ 20
0
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2
replies
1.6k
views
lfcShrink in DESeq2
deseq2 apeglm
updated 5.7 years ago by 43k • written 5.7 years ago by • 0
3
votes
3
replies
1.9k
views
Using alternative LFC shrinkage methods for computing p-values in DESeq2
deseq2 apeglm statistics
updated 5.9 years ago by 43k • written 5.9 years ago by • 0
3
votes
2
replies
2.0k
views
Calculate S/N ratios from apeglm for GSEA
apeglm fgsea Signal-To-Noise Ratio
updated 6.0 years ago by 43k • written 6.0 years ago by ▴ 20
2
votes
1
reply
1.2k
views
Deactivate svalue=T in lfcShrink - DESeq2 - apeglm
deseq2 apeglm
updated 6.1 years ago by 43k • written 6.1 years ago by ★ 4.8k
2
votes
4
replies
1.7k
views
What is the biological meaning of genes with FC = 0 after shrinkage
deseq2 apeglm
updated 6.1 years ago by 43k • written 6.1 years ago by • 0
0
votes
2
replies
3.4k
views
DESeq2 coefficients for APEGLM-shrinkage
deseq2 apeglm
updated 6.4 years ago by 43k • written 6.4 years ago by • 0
4
votes
4
replies
2.6k
views
Unexpected MAplot after apeglm shrinkage in DESeq2
apeglm deseq2 rna-seq
updated 6.5 years ago by 43k • written 6.5 years ago by ★ 4.8k
4
votes
2
replies
3.1k
views
Interpreting the results from lfcShrink() with apeglm in DESeq2
deseq2 apeglm lfcshrink
updated 6.6 years ago by 43k • written 6.6 years ago by ▴ 180
1
vote
4
replies
2.0k
views
Log2 fold-change shrinkage fails with lfcShrink when using the 'apeglm' method
deseq2 apeglm lfcshrink
6.8 years ago • updated 6.7 years ago coulsonr ▴ 20
0
votes
4
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1.5k
views
Error in Apeglm Method for Effect Size Shrinkage
deseq2 apeglm
updated 6.8 years ago by 43k • written 6.8 years ago by ▴ 40
10
votes
6
replies
7.1k
views
Log2FoldChange shrinkage method in DESeq2
deseq2 apeglm lfcshrink
updated 6.9 years ago by 43k • written 6.9 years ago by ▴ 90
41 results • Page 1 of 1
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Comment: How to left_join a tidySummarizedExperiment with a GRanges object by seqnames an by James W. MacDonald 68k
Have you figured out how to do this using tidy grammar? Using non-tidy grammar is quite simple, and perhaps you already know how to do that…
Comment: How can I correctly use phyloseq with Docker? by James W. MacDonald 68k
You can use [bioc-run][1] to simplify things as well. [1]: https://github.com/Bioconductor/bioc-run/tree/devel
Comment: How can I correctly use phyloseq with Docker? by James W. MacDonald 68k
You show how you modified the container, but not how you are running it, which is the critical part.
Comment: Discrepancies in normalised count data vs unnormalised by AMgroup • 0
Thank you for your reply. > Per sample all counts are scaled by the same size factor so I strongly assume that something was parsed here …
Comment: Discrepancies in normalised count data vs unnormalised by ATpoint ★ 4.8k
Please show examples using `plotCounts()`. Custom spreadsheets harbor the risk of parsing errors along the way which very often explains wh…
Votes
Answer: How to combine two DESeq2 objects (dds) for analysis
How to combine two DESeq2 objects (dds) for analysis
How can I correctly use phyloseq with Docker?
A: DESeq2::sizeFactors() function does not output the sizeFactor table.
Comment: Filtering after DESeq
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