Showing : apeglm • reset
0
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164
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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
793
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
replies
628
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
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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
779
views
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
replies
1.8k
views
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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962
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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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825
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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
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
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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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959
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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
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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
931
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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659
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
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1
reply
623
views
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
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
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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930
views
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
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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
reply
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
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
2.5k
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
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
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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
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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Answer: Reproducibility issue with scran together with lapply and BiocParallel by Aaron Lun ★ 28k
IIRC **BiocParallel** switches to a different RNG when inside its own functions like `bplapply` - specifically L'Ecuyer-CMRG, as opposed to…
Comment: DESeq2 output used for PCA plot on R studio by swbarnes2 ★ 1.3k
This looks terrible for RNASeq data, because it's not RNASeq data. It's a matrix of pretty random numbers, which you know because you poste…
Comment: DESeq2 output used for PCA plot on R studio by Aaliya • 0
I had taken this code from internet, but after reading about it and I did on my own, I would be making a post to ask for the suggestions if…
Comment: featureCounts reports an error:"featureCounts: input-files.c:2890: SAM_pairer_ge by shuwangxinze1996 • 0
Hello, I used 48 cpus and 320G of memory to run this program. My bam files size are 7-9G, wonder how much CPU and memory is enough? Thank …
Comment: DESeq2 output used for PCA plot on R studio by Kevin Blighe ★ 3.9k
This comment helps.
Votes
A: Are published RNA seq data analyses often wrong in calculating p-values and FDR?
A: How to explain how DESeq2 works to someone with zero bioinformatics background?
Answer: Interpret plot from DiffBind
Answer: How to retrieve gene ontology GO class from gene list?
Answer: How to retrieve gene ontology GO class from gene list?
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