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fastMNN reconstructed matrix
fastMNN
Interpretation
4.5 years ago
mloza
▴ 10
0
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1
reply
2.2k
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Low basemean and extremely high log2FC values, DESeq2
deseq2
interpretation
updated 5.8 years ago by
Michael Love
42k • written 5.8 years ago by
g.wang2
• 0
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1
reply
1.9k
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Pathview results interpretation
pathview
interpretation
6.5 years ago
Aurora
▴ 20
2
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11
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2.8k
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RNA degradation plot interpretation
xps
rnadegradationplot
interpretation
updated 8.7 years ago by
cstrato
★ 3.9k • written 8.7 years ago by
Biologist
▴ 120
4 results • Page
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Comment: ANOVA like approach of edgeR
by
Yunshun Chen
▴ 870
If you do it this way, the dispersion estimates would be much higher than they should (as the cell type difference is not accounted for in …
Comment: ANOVA like approach of edgeR
by
SamGG
▴ 350
Simply remove the cell type from the model. design <- model.matrix(~targets$Status)
Answer: ANOVA like approach of edgeR
by
Yunshun Chen
▴ 870
You could try the followings: > design <- model.matrix(~ 0 + group) > contrast <- makeContrasts(PvsL = 0.5*(L.pregnant + B.pregnan…
Answer: Identical samples after deseq2 batch effect removal
by
maripane
• 0
Thanks Michael, so is there a way to work around this issue? Can I somehow make sure I can remove this batch effects without overcorrecti…
Comment: CleanUpRNAseq with a GTF that is missing mitochondria annotation data
by
rcreed
• 0
The updated version worked well on my data. Thank you!
Votes
A: ANOVA-like test with edgeR
Answer: CleanUpRNAseq with a GTF that is missing mitochondria annotation data
Answer: CleanUpRNAseq with a GTF that is missing mitochondria annotation data
A: TopGO: How to retrieve the gene list related to a GO ID ?
A: Error in DESeqDataSet : some values in assay are not integers
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