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Limma
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5
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3
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672
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Limma-voom sample weights and impact on DEG numbers
limma
written 8 weeks ago by
A.Barden
▴ 20
4
votes
6
replies
1.7k
views
using limma trend workflow in CAMERA
CAMERA
limma
updated 14 days ago by
Gordon Smyth
53k • written 18 months ago by
Jiahao Tian
• 0
1
vote
4
replies
315
views
Bulk RNAseq analysis for
DESeq2
RNASeq
edgeR
limma
9 days ago • updated 8 days ago
Mariami
• 0
0
votes
2
replies
416
views
Combining two proteomics datasets with limpa
limpa
ProteomicsWorkflow
limma
6 weeks ago • updated 28 days ago
Andrew Pattison
• 0
0
votes
2
replies
50
views
Can sample-level weights be used when analysing GSVA scores in limma?
limma
updated 1 hour ago by
Robert Castelo
★ 3.4k • written 16 hours ago by
A.Barden
▴ 20
5 results • Page
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Comment: Can sample-level weights be used when analysing GSVA scores in limma?
by
Robert Castelo
★ 3.4k
Hi Gordon, thanks for giving your advice on how to use sample weights with GSVA scores. I have not used so far sample weights with GSVA sco…
Answer: Which preprocessing steps are needed before running limpa?
by
Gordon Smyth
53k
It looks to me that everything is working ok and limpa has done the right thing. You data has a lot of missing values, with the proportion …
Answer: Can sample-level weights be used when analysing GSVA scores in limma?
by
Gordon Smyth
53k
Yes, you could probably use the voom sample weights for an analysis of the GSVA scores for the same data, although I have never tried it. …
Comment: Why does IDTaxa trainingSet for SILVA contain "_2" suffixes in the taxonomy name
by
Erik Wright
▴ 160
You are correct. Thank you for noticing some of this 'pollution' with "_2" suffixes was unnecessary. I posted an updated SILVA classifier …
Comment: Which preprocessing steps are needed before running limpa?
by
miro165sabo
• 0
Hi @gordonsmyth, thank you a lot for very fast and valuable response. I edited the question to provide more details.
Votes
A: The meaning of results produced by the bamQC function implemented in the ATACseq
The meaning of results produced by the bamQC function implemented in the ATACseqQC
A: Reference paper or resource for limma::diffSplice and edgeR::diffSpliceDGE metho
Answer: Which preprocessing steps are needed before running limpa?
Answer: Should I use beta1 from limpa::dpc() or limpa::dpcCN(), if they differ?
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