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decidetests
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2
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5
replies
3.0k
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How to use q.value cutt off in "decideTests" function for RNAseq differential expression analysis
rnaseq
decideTests
limma
qvalue
8.9 years ago
anver
• 0
3
votes
2
replies
764
views
Is it ok to use decideTests on linearly dependent contrasts?
limma
decidetests
updated 5.5 years ago by
Gordon Smyth
50k • written 5.5 years ago by
Ryan C. Thompson
★ 7.9k
3
votes
4
replies
959
views
Discrepancy in the output of decideTests (total not equal to sum of up/down genes)
limma
decidetests
updated 7.5 years ago by
Gordon Smyth
50k • written 7.5 years ago by
ahmed.asadik
• 0
4
votes
5
replies
5.0k
views
decideTests() options in LIMMA
limma
B stats
decideTests
updated 20 months ago by
krushnach80
• 0 • written 9.0 years ago by
Elsa
• 0
5
votes
6
replies
1.4k
views
nestedF in decideTests: an analogue of Anova with post-hoc t-tests?
limma
anova
decidetests
updated 5.6 years ago by
Gordon Smyth
50k • written 5.6 years ago by
mikhael.manurung
▴ 270
4
votes
4
replies
1.2k
views
Correct use of Nested/Stage-wise testing with limma/stageR for 3-group design.
limma
stageR
decideTests
updated 5.3 years ago by
Koen Van den Berge
▴ 180 • written 5.3 years ago by
maltethodberg
▴ 170
0
votes
2
replies
722
views
decideTests vs topTable results
decideTests
topTable
limma
updated 10 months ago by
Gordon Smyth
50k • written 10 months ago by
Anna
▴ 20
0
votes
5
replies
1.2k
views
eBayes options and decideTests method
limma
eBayes
decideTests
topTable
updated 4.2 years ago by
Gordon Smyth
50k • written 4.2 years ago by
irene.roman
• 0
0
votes
1
reply
585
views
Decidetest results summary different from results written as .csv file
edgeR
voom
decidetests
DEG
updated 12 months ago by
Gordon Smyth
50k • written 12 months ago by
Ankita
• 0
3
votes
1
reply
1.2k
views
Limma -decideTests interpretation for M-values
limma
decidetests
methylation
updated 8.1 years ago by
Sean Davis
21k • written 8.1 years ago by
kraiczy
▴ 10
1
vote
3
replies
1.6k
views
limma decideTests results; how to get/sort most significant Genes?
limma
decidetests
updated 7.6 years ago by
Axel Klenk
★ 1.0k • written 7.6 years ago by
bi_Scholar
• 0
1
vote
2
replies
1.2k
views
limma decideTests global method with multiple groups
limma
decidetests
updated 6.5 years ago by
Aaron Lun
★ 28k • written 6.5 years ago by
jamie.gearing
▴ 60
12 results • Page
1 of 1
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Comment: Differential peaks that were not identified in diffbind were identified in diseq
by
lonn
• 0
I tried the default normalization and got similar results as above. Perhaps I need to try identifying the difference peak without using dif…
Answer: Cannabis and KEGGgraph
by
deeenes
▴ 30
Hello, I'm a developer of the `OmnipathR` package, and I wrote [a function][1] to access certain KEGG data: library(OmnipathR) cs…
Answer: RNAseq:Technical replicates from different batches
by
Gordon Smyth
50k
I am not entirely clear what you mean by "technical" replicates in this case. Are they resequencing of the same RNA samples or are they fre…
Comment: DMR.Plot shows error "Error in simpleLoess(y, x, w, span, degree = degree, param
by
russ.bainer
▴ 10
Hi, I'm hitting this too. As far as I can tell my DataTrack is fine, but perhaps I am missing something. Notably the same code works on o…
Comment: The difference when using Limma compare between 3 conditions vs 2 conditions
by
Chris
• 0
Hi Robert, If I don't want to use all pathway in c2 gene set but only a few pathways of interested, how can I do that? So we try to get a …
Votes
Installing/switching between versions of R/Rstudio/Bioconductor on personal machine (Linux | Ubuntu)
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Answer: OrgDb for maize
Comment: significant difference of p-values with dream() after updating VariancePartition
How to tell and visualize up/down regulation of pathways from clusterprofiler gsea output
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