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DESe
•
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0
votes
5
replies
395
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DESeq2 analysis
DESe
DESeq2
9 weeks ago • updated 8 weeks ago
Adèle
• 0
0
votes
2
replies
296
views
Handling NA's in Deseq2
Dese
DESeq2
3 months ago
Asger Mølgaard
• 0
2
votes
17
replies
880
views
lfcshrink error DESeq2
DESeq2
lfcshrink
DESe
updated 4 months ago by
Michael Love
40k • written 4 months ago by
Alina
• 0
2
votes
1
reply
277
views
Adding cell population estimates as a covariate in DESeq2 differential gene expression analysis
DESeq2
Dese
DifferentialRegulation
differe
updated 5 months ago by
Michael Love
40k • written 5 months ago by
Bernardo
▴ 10
3
votes
3
replies
725
views
Merging two plated in R
dese
DESeq2
updated 16 months ago by
James W. MacDonald
63k • written 16 months ago by
lmrogers34
▴ 10
0
votes
5
replies
2.5k
views
Error in DESeqDataSet(se, design = design, ignoreRank) : all variables in design formula must be columns in colData
DESE
DESeq2
updated 16 months ago by
Basti
▴ 720 • written 16 months ago by
Maryam.sed1400
• 0
1
vote
3
replies
1.1k
views
ERROR: unable to find an inherited method for function ‘dispersions<-’ for signature ‘"DESeqDataSet",
DESeq2
dese
20 months ago
aedavids
▴ 20
0
votes
2
replies
641
views
DESeq2 ratio of ratios and p-value
DESeq2
dese
23 months ago
wilfried.guiblet
• 0
0
votes
2
replies
456
views
where the gene is overexpressed and down regulated while doing DESeq2 analysis
DESe
DESeq2
updated 23 months ago by
Michael Love
40k • written 23 months ago by
Dinesh
• 0
2
votes
3
replies
795
views
Single sided P-value for DESeq2 Likelihood Ratio Test
DESeq2
DESe
updated 2.6 years ago by
Michael Love
40k • written 2.6 years ago by
glennli
• 0
0
votes
2
replies
588
views
Effect of within-group variation on gene expression analysis
DESeq2
updated 2.8 years ago by
Michael Love
40k • written 2.8 years ago by
hpapoli
• 0
11 results • Page
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Answer: Deseq2 calculated log2foldchange not consistent with RPM in IP-small RNA-seq
by
Michael Love
40k
Did you manually calculate RPMs? Try `fpm(dds)` for comparison, as this also uses DESeq2 median ratio scaling.
Comment: collapseReplicates error after tximeta
by
Michael Love
40k
A note: I've now changed collapseReplicates() to output a loud warning when it is run on a DESeqDataSet (SummarizedExperiment) with more th…
Comment: Suggested package missing from Development version of Bioconductor
by
shepherl
3.5k
Have you tried reaching out to the maintainers? If they do not fix the package it will remain unavailable and cause ERROR in your package.…
Answer: Batch effect adjust in model matrix
by
ATpoint
★ 3.4k
Each sample is a different day, that is called "nested", so there is nothing you can do here. Next time do a better experimental design, he…
Comment: Does countsFromAbundance="lengthScaledTPM" produce un-normalized counts?
by
Michael Love
40k
Oh, I see. If you can't use counts + offset then I prefer lengthScaledTPM to DESeq2, i.e. `txi$counts` to `DESeqDataSetFromMatrix()`. So …
Votes
Comment: Batch correction and repeated measures
batch effect : comBat or blocking in limma ?
Batch correction and repeated measures
Comment: Does countsFromAbundance="lengthScaledTPM" produce un-normalized counts?
Comment: Phenotype effect - building a contrast matrix - grouping vs interaction
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Gordon Smyth
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James W. MacDonald
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nhaus
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▴ 660
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Michael Love
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