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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
991
views
Ashr and IHW
Ashr
LFCShrinkage
IHW
DESeq2
2.3 years ago
Bex
• 0
2
votes
1
reply
875
views
padj NA after shrinking log2FC (DESeq2)
deseq2
ashr
3.6 years ago
da.de
▴ 30
2
votes
2
replies
890
views
Negative svalues from DESeq2 lfcShrink with ashr
ashr
DESeq2
lfcShrink
svalue
3.1 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
628
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
630
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
Recent ...
Replies
Comment: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
by
Alexandre
• 0
Hello James, Thank you very much for your answer and taking the time to read my post. I understand your remark, but isn't the approach o…
Comment: PCA plot suggestions
by
JKim
• 0
cross post: https://www.biostars.org/p/9593486/
Answer: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
by
James W. MacDonald
65k
You cannot correct for technical variability due to batch if samples are nested in batch. The technical and biological differences are comp…
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2)
by
James W. MacDonald
65k
You will need to show some reproducible code for anybody to track this down. Please note that `DESeq2` has been used by thousands of people…
Comment: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
by
Alexandre
• 0
My code for the sessionInfo() . If the pictures are too big, I will downsize them. THank you again for reading my post ! ```r > sessionInf…
Votes
Answer: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
Answer: Use of negative binomial model for exponential decay rate estimation using DESeq
C: null model and DEXSeqDataSet object in DEXSEQ
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?
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