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DESe
•
reset
0
votes
3
replies
589
views
DESeq2 Results in Different Pvalue & Log2FC using the same code and data
DESeq2
dese
written 13 months ago by
Xu
• 0
2
votes
2
replies
586
views
Why is the inclusion of RUVs not reflected in the EDA plots produced from normalised counts extracted from deseq2?
RUVSeq
DESeq2
dese
7 months ago
BioinfGuru
▴ 70
4
votes
5
replies
1.9k
views
Adding cell population estimates as a covariate in DESeq2 differential gene expression analysis
DESeq2
Dese
DifferentialRegulation
differe
updated 9 months ago by
ij283
• 0 • written 23 months ago by
Bernardo
▴ 10
0
votes
1
reply
414
views
collapseReplicates dimension error
DESeq2
Dese
updated 11 months ago by
Michael Love
43k • written 12 months ago by
Léa
• 0
0
votes
2
replies
603
views
Cross-species analysis using DESeq2 - size factor computation
dese
DESeq2
13 months ago
pl23
• 0
0
votes
2
replies
911
views
Linear Model Fitting and Colinearity
dese
DESeq2
15 months ago
Hugo
• 0
0
votes
5
replies
1.2k
views
DESeq2 analysis
DESe
DESeq2
20 months ago • updated 19 months ago
Adèle
• 0
0
votes
2
replies
1.9k
views
Handling NA's in Deseq2
Dese
DESeq2
21 months ago
Asger Mølgaard
• 0
2
votes
17
replies
2.8k
views
lfcshrink error DESeq2
DESeq2
lfcshrink
DESe
updated 22 months ago by
Michael Love
43k • written 22 months ago by
Alina
• 0
3
votes
3
replies
1.2k
views
Merging two plated in R
dese
DESeq2
updated 2.8 years ago by
James W. MacDonald
68k • written 2.8 years ago by
lmrogers34
▴ 10
0
votes
5
replies
4.2k
views
Error in DESeqDataSet(se, design = design, ignoreRank) : all variables in design formula must be columns in colData
DESE
DESeq2
updated 2.9 years ago by
Basti
▴ 780 • written 2.9 years ago by
Maryam.sed1400
• 0
1
vote
3
replies
1.8k
views
ERROR: unable to find an inherited method for function ‘dispersions<-’ for signature ‘"DESeqDataSet",
DESeq2
dese
3.1 years ago
aedavids
▴ 20
0
votes
2
replies
1.1k
views
DESeq2 ratio of ratios and p-value
DESeq2
dese
3.4 years ago
wilfried.guiblet
• 0
0
votes
2
replies
825
views
where the gene is overexpressed and down regulated while doing DESeq2 analysis
DESe
DESeq2
updated 3.4 years ago by
Michael Love
43k • written 3.4 years ago by
Dinesh
• 0
2
votes
3
replies
1.2k
views
Single sided P-value for DESeq2 Likelihood Ratio Test
DESeq2
DESe
updated 4.1 years ago by
Michael Love
43k • written 4.1 years ago by
glennli
• 0
0
votes
2
replies
1.1k
views
Effect of within-group variation on gene expression analysis
DESeq2
updated 4.3 years ago by
Michael Love
43k • written 4.3 years ago by
hpapoli
• 0
16 results • Page
1 of 1
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Comment: Loading Ensembl 98 EnsDb from Annotation Hub fails with database disk image malf
by
earntodiesaz
• 0
I'm delighted to have the chance to engage in conversation with your blog; I'm looking forward to reading more posts that can be relied upo…
Comment: Guidance Needed: Best Practices for Handling Technical Replicates in RNA-seq Ana
by
earntodiesaz
• 0
To be honest with you, I must say that it was an exceptionally good post. Writing it down and reading it during my lunch break was a very e…
Comment: Using edgeR::voomLmFit for the analysis of paired clinical RNA-seq samples with
by
Gordon Smyth
52k
I generally recommend `block=individual` for unbalanced designs, to recover information from incomplete blocks. I would only be disuaded fr…
Comment: Using edgeR::voomLmFit for the analysis of paired clinical RNA-seq samples with
by
Devin
▴ 10
Thank you, Gordon, for your responses to all of my questions. For analysis A), in the case when a patient has either a missing timepoint or…
Comment: Using TPM from tximport of Salmon output for singscore
by
Kent
• 0
Thanks Michael. Just out of curiosity, would you also use the same technique for things like clustering analysis or when looking at the abn…
Votes
Comment: Using edgeR::voomLmFit for the analysis of paired clinical RNA-seq samples with
Answer: Using edgeR::voomLmFit for the analysis of paired clinical RNA-seq samples with
Answer: Using edgeR::voomLmFit for the analysis of paired clinical RNA-seq samples with
Answer: Using TPM from tximport of Salmon output for singscore
Comment: Using TPM from tximport of Salmon output for singscore
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Luca
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Hervé Pagès
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Michael Love
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James W. MacDonald
68k
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