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DESE
•
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2
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2
replies
941
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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
631
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
912
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
981
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
1 of 1
Recent ...
Replies
Comment: Combining two proteomics datasets with limpa
by
Andrew Pattison
• 0
Thanks heaps Gordon. I went with option 1 and no normalisation and all seems to have worked well. Cheers, Andrew
Comment: limpa-blank normalization and Spectronaut's PTM stoichiometry
by
Gordon Smyth
53k
Flagging protein groups as likely contaminants in this way will be fine for a limpa analysis. The `Cont_` proteins can optionally stay in f…
Answer: Making a Full Rank Model for Allele-Specific Expression with DESeq2
by
Gordon Smyth
53k
Aaron Lun was a PhD student in my Lab back in 2015, when he posted the answers about allele-specific expression that you and Mike Love have…
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…
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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