Showing : ApeGLM • reset
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How to run allelic imbalance in apeglm
apeglm
8 hours ago euge.eugenio ▴ 20
0
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1
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216
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lfcShrink error: the line search routine failed
apeglm DESeq2
updated 9 weeks ago by 42k • written 9 weeks ago by • 0
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2
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881
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Error: insufficient numeric precision during Log fold change shrinkage with apeglm
apeglm
updated 8 months ago by 42k • written 9 months ago by • 0
0
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4
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674
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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 10 months ago by 42k • written 10 months ago by ▴ 20
2
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7
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1.9k
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optimHess problem in apeglm/DESeq2
DESeq2 apeglm
updated 12 months ago by 42k • written 12 months ago by ★ 4.1k
3
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2
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823
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DESeq2 lfcShrink: swapping reference gives different results for the same comparison
DESeq2 apeglm
14 months ago • updated 13 months ago Daphnia • 0
1
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5
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1.9k
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DESeq2 outlier options and LFC Shrinkage
DESeq2 RNASeq RnaSeqSampleSize apeglm
updated 21 months ago by 42k • written 21 months ago by • 0
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3
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1.0k
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LFC shrinkage setting negative LFC svalues to zero
DESeq2 DifferentialExpression apeglm
updated 22 months ago by 42k • written 22 months ago by • 0
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2
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849
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running apeglm on a normal model and multiple coefficients
shrinkage apeglm
2.1 years ago Frederik Ziebell ▴ 20
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2
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1.2k
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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
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3
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1.6k
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Choosing an svalue threshold from apeglm shrunken results in DESeq2
apeglm DESeq2
updated 2.7 years ago by 42k • written 2.7 years ago by ▴ 40
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5
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1.4k
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lfcShrink probelm in many 0 count genes RNA-seq data
ashr DESeq2 apeglm
updated 2.7 years ago by 42k • written 2.8 years ago by ▴ 40
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1
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711
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Non-significant but high LFC after apeglm shrinkage
DESeq2 apeglm
updated 3.2 years ago by 42k • written 3.2 years ago by • 0
0
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1
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997
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Plotting the most expressed genes after conducting DESeq2
DESeq2 pheatmap apeglm
updated 3.3 years ago by 42k • written 3.3 years ago by ▴ 10
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2
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1.2k
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DESeq2 in R
DESeq2 apeglm
updated 3.3 years ago by ★ 1.4k • written 3.3 years ago by ▴ 10
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2
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1.3k
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DSEQ apeglm
DESeq2 apeglm
3.3 years ago amoaristotle ▴ 10
2
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1
reply
1.1k
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apeglm -- influence of reference level on logFC and svalues
DESeq2 apeglm
updated 3.3 years ago by 42k • written 3.3 years ago by ★ 4.1k
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3
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1.0k
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Using altHypothesis on apleglm-shrunken log2FoldChanges
apeglm DESeq2
3.4 years ago zefrieira • 0
0
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1
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958
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DESeq2 - shrunken LFC calculation
apeglm DESeq2
updated 3.4 years ago by 42k • written 3.4 years ago by ▴ 50
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3
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671
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Influence of DEG in ASE analysis within apeglm
apeglm
updated 3.6 years ago by 42k • written 3.6 years ago by • 0
1
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1
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631
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Exceeding Over-dispersion parameter bbEstDisp
apeglm bbEstdisp allele ratio
updated 3.7 years ago by 42k • written 3.7 years ago by • 0
5
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10
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1.3k
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Allelic imbalance in apeglm
apeglm Allelic imbalance concept
updated 3.7 years ago by 42k • written 3.7 years ago by • 0
1
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4
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1.7k
views
Using different LFC shrinkage estimators for spike-in normalised RNA-seq data
deseq2 apeglm rna-seq spike-in
updated 3.8 years ago by 42k • written 3.8 years ago by ▴ 10
3
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2
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1.9k
views
lfcShrink function in DEseq2 and s-values
deseq2 apeglm
updated 3.8 years ago by 42k • written 3.8 years ago by ▴ 10
2
votes
1
reply
682
views
What are the steps to use a complex model of Allelic imbalance through apeglm
apeglm complex model ASE Allelic imbalance
updated 3.8 years ago by 42k • written 3.8 years ago by • 0
1
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1
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814
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Why s-values instead of p-values with non-default lfcThreshold and apeglm shrinkage in DESeq2
deseq2 apeglm
updated 3.9 years ago by 42k • written 3.9 years ago by • 0
3
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4
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2.2k
views
Reporting S values? Reporting padj values?
deseq2 apeglm
updated 4.0 years ago by 42k • written 4.0 years ago by ▴ 20
4
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4
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2.5k
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RNA seq analysis using Deseq2 and apeglm lfc shrinkage
deseq2 fdrtool apeglm
updated 4.1 years ago by 42k • written 4.1 years ago by • 0
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2
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950
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Coefficient names for multiple group comparisons to use with lfcShrink & apeglm
deseq2 lfcShrink apeglm
updated 4.4 years ago by 42k • written 4.4 years ago by ▴ 20
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2
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1.3k
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lfcShrink in DESeq2
deseq2 apeglm
updated 4.8 years ago by 42k • written 4.8 years ago by • 0
3
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3
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1.4k
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Using alternative LFC shrinkage methods for computing p-values in DESeq2
deseq2 apeglm statistics
updated 5.0 years ago by 42k • written 5.0 years ago by • 0
3
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2
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1.4k
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Calculate S/N ratios from apeglm for GSEA
apeglm fgsea Signal-To-Noise Ratio
updated 5.0 years ago by 42k • written 5.0 years ago by ▴ 20
2
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1
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980
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Deactivate svalue=T in lfcShrink - DESeq2 - apeglm
deseq2 apeglm
updated 5.1 years ago by 42k • written 5.1 years ago by ★ 4.1k
2
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4
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1.3k
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What is the biological meaning of genes with FC = 0 after shrinkage
deseq2 apeglm
updated 5.2 years ago by 42k • written 5.2 years ago by • 0
0
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2
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2.7k
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DESeq2 coefficients for APEGLM-shrinkage
deseq2 apeglm
updated 5.5 years ago by 42k • written 5.5 years ago by • 0
4
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4
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2.1k
views
Unexpected MAplot after apeglm shrinkage in DESeq2
apeglm deseq2 rna-seq
updated 5.6 years ago by 42k • written 5.6 years ago by ★ 4.1k
4
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2
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2.6k
views
Interpreting the results from lfcShrink() with apeglm in DESeq2
deseq2 apeglm lfcshrink
updated 5.6 years ago by 42k • written 5.6 years ago by ▴ 160
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4
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1.6k
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Log2 fold-change shrinkage fails with lfcShrink when using the 'apeglm' method
deseq2 apeglm lfcshrink
5.8 years ago coulsonr ▴ 20
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4
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1.2k
views
Error in Apeglm Method for Effect Size Shrinkage
deseq2 apeglm
updated 5.9 years ago by 42k • written 5.9 years ago by ▴ 40
10
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6
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5.4k
views
Log2FoldChange shrinkage method in DESeq2
deseq2 apeglm lfcshrink
updated 6.0 years ago by 42k • written 6.0 years ago by ▴ 90
40 results • Page 1 of 1
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Comment: all variables in design formula must be columns in colData (Deseq2) error by Galina • 0
thank you!
Comment: all variables in design formula must be columns in colData (Deseq2) error by ATpoint ★ 4.1k
coldata_rat <- data.frame(conditions=..., batch=...)
Answer: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it by robersy • 0
Thank you all for your comments. I will follow your suggestions.
Comment: Numerical differences in DESeq2 output depending on different design matrix cons by Ken C • 0
Hi Michael, thanks a lot for your prompt reply! Not sure if this is appropriate or if you are the right person to ask -- is there anything…
Comment: Numerical differences in DESeq2 output depending on different design matrix cons by Ken C • 0
Well, if I look at genes with baseMean>50, then the relative absolute difference in log2FoldChange (say over the absolute log2FoldChange of…
Votes
biomaRt not working - lazy table error
Answer: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
Comment: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
Answer: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
Comment: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
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