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Ashr
•
reset
3
votes
4
replies
1.5k
views
Massive L2FC in DESeq2
deseq2
ashr
rna-seq
4.0 years ago
Alex
• 0
2
votes
2
replies
1.0k
views
Ashr and IHW
Ashr
LFCShrinkage
IHW
DESeq2
2.4 years ago • updated 2.3 years ago
Bex
• 0
2
votes
1
reply
887
views
padj NA after shrinking log2FC (DESeq2)
deseq2
ashr
3.6 years ago
da.de
▴ 30
2
votes
2
replies
905
views
Negative svalues from DESeq2 lfcShrink with ashr
ashr
DESeq2
lfcShrink
svalue
3.2 years ago
Enrico
• 0
1
vote
5
replies
1.4k
views
lfcShrink probelm in many 0 count genes RNA-seq data
ashr
DESeq2
apeglm
updated 2.7 years ago by
Michael Love
41k • written 2.7 years ago by
Guandong Shang
▴ 40
0
votes
5
replies
2.0k
views
Deseq2, lfcThreshold .
ashr
Deseq2
lfcThreshold
updated 2.6 years ago by
Michael Love
41k • written 4.0 years ago by
Iryna
• 0
0
votes
2
replies
634
views
Ashr error: Optimization failed to converge. Results may be unreliable. Try increasing maxiter and rerunning.
ashr
4.0 years ago
kavator
▴ 30
0
votes
4
replies
658
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
Michael Love
41k • written 9 months ago by
Ndimensional
▴ 20
8 results • Page
1 of 1
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Replies
Answer: How to use bootRanges to bootstrap small RNA loci (nullranges package)
by
Poonam
• 0
Hi Michael, I think there is something wrong with the generation of nullranges. I was working with small RNA and methylation overlaps. …
Answer: Once again a "Model matrix not full rank"
by
swbarnes2
★ 1.3k
Replicate numbers, like the 1 in control_1 are fine in sample names, but never add them to anything else in colData. From the computer's p…
Answer: limma Intercept vs No-intercept models completely changing DMR results?
by
Gordon Smyth
50k
I'll add a little bit of general advice to James' answer. You seem to have the misunderstanding that you can change the design matrix but …
Answer: package goseq seems to be not available on the latest version of R
by
Gordon Smyth
50k
It is true that goseq isn't available for Bioc 3.19 (as at 4 May 2024). In the meantime, you could consider using the goana() and kegga() …
Answer: limma Intercept vs No-intercept models completely changing DMR results?
by
James W. MacDonald
65k
This part: ``` design_intercept <- model.matrix(~Alt+Sex+Age+PC1, data=targets_Sherpa) colnames(design_intercept) <- c("AltSHP_LA","Al…
Votes
Answer: Why does GSEA on edgeR results for randomized samples give highly significant p-
Answer: limma Intercept vs No-intercept models completely changing DMR results?
Answer: CombineArrays for EPIC and EPIC V2
Answer: Too many significant genes when integrating gtex and tcga
Comment: Too many significant genes when integrating gtex and tcga
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