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DESe
•
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2
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2
replies
940
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Why is the inclusion of RUVs not reflected in the EDA plots produced from normalised counts extracted from deseq2?
RUVSeq
DESeq2
dese
17 months ago
BioinfGuru
▴ 70
0
votes
1
reply
630
views
collapseReplicates dimension error
DESeq2
Dese
updated 22 months ago by
Michael Love
43k • written 22 months ago by
Léa
• 0
0
votes
3
replies
797
views
DESeq2 Results in Different Pvalue & Log2FC using the same code and data
DESeq2
dese
written 23 months ago by
Xu
• 0
0
votes
2
replies
911
views
Cross-species analysis using DESeq2 - size factor computation
dese
DESeq2
24 months ago
pl23
• 0
0
votes
2
replies
1.2k
views
Linear Model Fitting and Colinearity
dese
DESeq2
2.1 years ago
Hugo
• 0
0
votes
5
replies
1.5k
views
DESeq2 analysis
DESe
DESeq2
2.5 years ago
Adèle
• 0
0
votes
2
replies
2.4k
views
Handling NA's in Deseq2
Dese
DESeq2
2.6 years ago
Asger Mølgaard
• 0
2
votes
17
replies
3.5k
views
lfcshrink error DESeq2
DESeq2
lfcshrink
DESe
updated 2.7 years ago by
Michael Love
43k • written 2.7 years ago by
Alina
• 0
4
votes
5
replies
2.3k
views
Adding cell population estimates as a covariate in DESeq2 differential gene expression analysis
DESeq2
Dese
DifferentialRegulation
differe
updated 19 months ago by
ij283
• 0 • written 2.8 years ago by
Bernardo
▴ 10
3
votes
3
replies
1.4k
views
Merging two plated in R
dese
DESeq2
updated 3.7 years ago by
James W. MacDonald
68k • written 3.7 years ago by
lmrogers34
▴ 10
0
votes
5
replies
4.7k
views
Error in DESeqDataSet(se, design = design, ignoreRank) : all variables in design formula must be columns in colData
DESE
DESeq2
updated 3.7 years ago by
Basti
▴ 780 • written 3.7 years ago by
Maryam.sed1400
• 0
1
vote
3
replies
2.1k
views
ERROR: unable to find an inherited method for function ‘dispersions<-’ for signature ‘"DESeqDataSet",
DESeq2
dese
4.0 years ago
aedavids
▴ 20
0
votes
2
replies
1.3k
views
DESeq2 ratio of ratios and p-value
DESeq2
dese
4.2 years ago
wilfried.guiblet
• 0
0
votes
2
replies
979
views
where the gene is overexpressed and down regulated while doing DESeq2 analysis
DESe
DESeq2
updated 4.3 years ago by
Michael Love
43k • written 4.3 years ago by
Dinesh
• 0
2
votes
3
replies
1.5k
views
Single sided P-value for DESeq2 Likelihood Ratio Test
DESeq2
DESe
updated 4.9 years ago by
Michael Love
43k • written 4.9 years ago by
glennli
• 0
0
votes
2
replies
1.4k
views
Effect of within-group variation on gene expression analysis
DESeq2
updated 5.2 years ago by
Michael Love
43k • written 5.2 years ago by
hpapoli
• 0
16 results • Page
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Recent ...
Replies
Comment: Making a Full Rank Model for Allele-Specific Expression with DESeq2
by
Michael Love
43k
You just need the mouse identifier (controls baseline) and the group specific allelic effect.
Comment: limpa-blank normalization and Spectronaut's PTM stoichiometry
by
Julia Broadbent
• 0
Hi Emily, Just sharing a resource for handling contaminants - we use the methods described in [Frankenfield et al. (2022)](https://pubs.acs…
Comment: Making a Full Rank Model for Allele-Specific Expression with DESeq2
by
Michael Love
43k
You may want to speak with a local statistician, because you don't just want to find the first full rank matrix and run with that if it doe…
Comment: limpa-blank normalization and Spectronaut's PTM stoichiometry
by
Gordon Smyth
53k
It is fine for your mass spec facility to include blank samples as part of their internal QC, but such samples should not in my opinion be …
Comment: Making a Full Rank Model for Allele-Specific Expression with DESeq2
by
chp265
• 0
Hm, okay, in building a fake model by hand I think I'm realizing the problem: `mouse` and its variants are ideally acting as basically a ra…
Votes
A: Filtering read counts matrix: how to deal with duplicated gene symbols, differen
Comment: limpa analysis advice
Answer: When to use edgeR or limma
Answer: When to use edgeR or limma
Answer: When to use edgeR or limma
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