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Controls
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Running DESeq2 on viral infection without control/host data
DESeq2
viral
controls
3.3 years ago • updated 3.2 years ago
f99942
• 0
0
votes
8
replies
2.9k
views
Two controls in RNAseq formula for DESeq2
deseq2
formula
controls
design
updated 6.4 years ago by
Michael Love
43k • written 6.4 years ago by
taveluz
• 0
1
vote
3
replies
6.2k
views
DESeq2 estimateSizeFactors with control genes
deseq2
differential gene expression
controls
references
updated 10 months ago by
sofia.rigou
• 0 • written 7.1 years ago by
cris.kgs
• 0
0
votes
2
replies
1.5k
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How can I define which samples are controls and which samples are cases in ChAMP
ChAMP
champ.DMP
Cases
Controls
references
7.3 years ago
yuabrahamliu
• 0
4 results • Page
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Comment: BiocParallel (and DESeq2) - wrong args for environment subassignment
by
ATpoint
★ 5.0k
Yes, still it's not reproducible, yet hard to debug. I cannot reproduce myself either.
Comment: BiocParallel (and DESeq2) - wrong args for environment subassignment
by
Benjamin
• 0
Still happening using pre-existing size factors estimating dispersions gene-wise dispersion estimates: 15 workers mean-dis…
Answer: BiocParallel (and DESeq2) - wrong args for environment subassignment
by
Benjamin
• 0
Still happening in a clean install
Comment: limpa analysis advice
by
Gordon Smyth
53k
Yes, we use Astral currently. The main dataset in the limpa preprint is Astral. I don't see any major problems with your data and I think …
Comment: limpa analysis advice
by
SamGG
▴ 360
Thank you for your comments. Please note that I did not apply any filtering to the peptide intensity. The experimental protocol includes tw…
Votes
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
Answer: When to use edgeR or limma
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