Showing : apeglm • reset
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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
792
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
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4
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627
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
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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
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2
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777
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DESeq2 lfcShrink: swapping reference gives different results for the same comparison
DESeq2 apeglm
13 months ago • updated 12 months ago Daphnia • 0
1
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5
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1.8k
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DESeq2 outlier options and LFC Shrinkage
DESeq2 RNASeq RnaSeqSampleSize apeglm
updated 20 months ago by 41k • written 21 months ago by • 0
1
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3
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961
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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
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824
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running apeglm on a normal model and multiple coefficients
shrinkage apeglm
24 months ago Frederik Ziebell ▴ 20
1
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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
1
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3
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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
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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 41k • written 2.7 years ago by ▴ 40
0
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1
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693
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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
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1
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957
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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
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2
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1.1k
views
DESeq2 in R
DESeq2 apeglm
updated 3.2 years ago by ★ 1.3k • written 3.2 years ago by ▴ 10
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2
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1.2k
views
DSEQ apeglm
DESeq2 apeglm
3.2 years ago amoaristotle ▴ 10
2
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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
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990
views
Using altHypothesis on apleglm-shrunken log2FoldChanges
apeglm DESeq2
3.3 years ago zefrieira • 0
0
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1
reply
930
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
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658
views
Influence of DEG in ASE analysis within apeglm
apeglm
updated 3.5 years ago by 41k • written 3.6 years ago by • 0
1
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1
reply
623
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Exceeding Over-dispersion parameter bbEstDisp
apeglm bbEstdisp allele ratio
updated 3.6 years ago by 41k • written 3.6 years ago by • 0
5
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10
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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
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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 3.7 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
662
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
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1
reply
790
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
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4
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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
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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
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2
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929
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Coefficient names for multiple group comparisons to use with lfcShrink & apeglm
deseq2 lfcShrink apeglm
updated 4.3 years ago by 41k • written 4.3 years ago by ▴ 20
0
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2
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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
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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
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1
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962
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
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4
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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
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2
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2.6k
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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
2.5k
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
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4
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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
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4
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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
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6
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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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Answer: DESEQ2 IHW and Apelgm method for Shrinkage (adding s values to FDR) by Michael Love 41k
> I got many p values that had "1.000000e+00" and padj "1" and stat of "0" when I added the Log threshold of LFC >1 and LFC < -1...is this …
Comment: Trying to use enrichGO by fernanda.backsouza ▴ 10
With all my love, thank you Guido, GOxploreR beeing a big ally for me. I don't know how to be grateful right now.
Comment: DESeq2 output used for PCA plot on R studio by swbarnes2 ★ 1.3k
You didn't generate it with an experiment, you made it up: Your PCA doesn't look like a good RNASeq experiment, because it's not.
Answer: Opposite sign of LFC in count plots of DEGs (DESeq2) by swbarnes2 ★ 1.3k
Your contrast is comparing LGR5 to Homeostasis. The bottom 2 are fine, it's the top one that is wrong. Are you sure this step isn't misla…
Comment: get BM error by James W. MacDonald 65k
I believe you need NCBI Gene IDs for KEGG, in which case you may need to map. The three genes you have shown here don't map, and of those t…
Votes
C: when to apply quantile normalization with voom in limma/voom framework with RNA-
A: How to know if I should use voomWithQualityWeights() or not?
A: Weird results (ribosomal proteins / Y-linked genes) in limma/voom
Answer: Log-cpm values from limma
Answer: Log-cpm values from limma
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