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significance
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reset
1
vote
8
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5.0k
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DESeq2: betaPrior changes significance dramatically
deseq2
betaPrior
shrinkage
significance
7.5 years ago
brynedal
▴ 40
1
vote
1
reply
2.4k
views
Beta Value Analysis - DNA Methylation Dataset
dna methylation
illimina 450k methylation
beta
M
significance
updated 8.1 years ago by
James W. MacDonald
68k • written 8.1 years ago by
skids121
• 0
3
votes
3
replies
1.4k
views
limma decideTests: only p-value less than (but not equal to) alpha are flagged as significant
limma
edger
significance
rnaseq
updated 8.6 years ago by
Gordon Smyth
53k • written 8.7 years ago by
roberto.spreafico
▴ 20
1
vote
4
replies
1.8k
views
comparing transcripts expression between conditions
salmon
transcripts
significance
counts
9.3 years ago
Assa Yeroslaviz
★ 1.5k
0
votes
3
replies
3.2k
views
Wald vs LRT: different number of significant genes when testing the same coefficient
deseq2
wald
lrt
genes
significance
updated 9.4 years ago by
Michael Love
43k • written 9.4 years ago by
aziza
▴ 20
0
votes
0
replies
1.1k
views
cell analysis- significance output perturbed in shiny environment
cellcode
significance
9.5 years ago
christopher.clarskon15
▴ 20
6 results • Page
1 of 1
Recent ...
Replies
Comment: DESeq2 for candidate gene analysis
by
piffelpaff
▴ 10
thank you so much for answering Dr. Love!
Answer: DESeq2 for candidate gene analysis
by
Michael Love
43k
Your plan 1 is reasonable. Run DESeq2 on the whole dataset to obtain size factors and moderated dispersion estimates and then extract the u…
Comment: Best practice for handling large data (matrix with >2^31-1 non-zero elements) in
by
James W. MacDonald
68k
Oh. ``` > z <- read10xCounts(c(tmpdir, tmpdir), mtx.class = "SVT_SparseMatrix", delayed = TRUE) > class(counts(z)) [1] "DelayedMatrix" att…
Comment: Best practice for handling large data (matrix with >2^31-1 non-zero elements) in
by
James W. MacDonald
68k
That's weird. Using the example data works for me. ``` > example(read10xCounts) rd10xC> # Mocking up some 10X genomics output. rd10xC> ex…
Comment: Join BOC Sciences at Drug Discovery Chemistry
by
teamardigen
• 0
Sounds like an exciting event for anyone passionate about small molecule innovation. The focus on discovery and optimization really drives …
Votes
Answer: DESeq2 for candidate gene analysis
DESeq2 for candidate gene analysis
Join BOC Sciences at Drug Discovery Chemistry
Drug datasets for RNA-seq
Comment: Check removeBatchEffect effectiveness
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