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multiple groups
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0
votes
2
replies
1.4k
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Differential expression between multiple groups
multiple groups
differential gene expression
microarray
5.2 years ago
A
▴ 40
0
votes
8
replies
1.1k
views
edgeR: multi-subject time series analysis
timecourse
multiple groups
edgeR
updated 5.2 years ago by
Aaron Lun
★ 28k • written 5.2 years ago by
BharathAnanth
▴ 70
1
vote
3
replies
703
views
DESEq2: the use of interaction term and grouping with different betaPrior arguments in older version of DESEq2
deseq2
interaction term
multiple groups
betaprior
updated 4.7 years ago by
Michael Love
39k • written 4.7 years ago by
tarun2
• 0
0
votes
3
replies
615
views
Group comparison using DESeq
deseq2
multiple groups
updated 4.8 years ago by
James W. MacDonald
62k • written 4.8 years ago by
amir_b_e
• 0
0
votes
1
reply
594
views
Changing group labels yields different results in DESeq2
deseq2
multiple groups
updated 4.9 years ago by
Michael Love
39k • written 4.9 years ago by
blobbyscience
• 0
5 results • Page
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Answer: msPurity::spectralMatching Error in getSmeta(con, pids) : No meta data for spect
by
thomas.nigel.lawson
• 0
This has been resolved (Windows Firewall issue) - see github issue https://github.com/computational-metabolomics/msPurity/issues/100
Answer: DESeq2 parameter infernce
by
Michael Love
39k
We use IRLS which is related to Newton-Raphson method. I suppose you can use any optimization method you prefer. We also sometimes use L-BF…
Answer: DESeq2 with 2 continuous factors, LRT, coeficients and slope
by
Michael Love
39k
See `?results` which describes what the LFC is when you perform an LRT: "*For analyses using the likelihood ratio test*..." Also in the …
Answer: DESeq2 with sample effect, unequal sample sizes
by
Michael Love
39k
For statistical analysis plans such as design and coefficient interpretation, I recommend collaborating with a local statistician or someon…
Comment: Bioconductor tool for curating annotations?
by
Lluís Revilla Sancho
▴ 700
I think you can find those transcripts not overlapping with a GRanges object easily via ?GenomicRanges::setdiff, but I don't know how to an…
Votes
Answer: AnnotationForge::makeOrgPackage "argument is missing, with no default" Errors
Comment: Error in .order_seqlevels(chrom_sizes[, "chrom"]) : !anyNA(m32) is not TRUE
Comment: Error in .order_seqlevels(chrom_sizes[, "chrom"]) : !anyNA(m32) is not TRUE
Answer: Limma-voom with inverse probability weights
A: Limma-voom with external observation weights
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