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13
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Using edgeR or DESeq2 to analyze allele-specific expression?
edgeR
deseq2
ase
allele
8.6 years ago
trianglescout
▴ 40
1
vote
3
replies
1.1k
views
DESeq2 for ASE
DESEQ2
ASE
diploid-genome
updated 6.6 years ago by
Michael Love
42k • written 6.6 years ago by
gtechbio
▴ 10
2
votes
1
reply
672
views
What are the steps to use a complex model of Allelic imbalance through apeglm
apeglm
complex model
ASE
Allelic imbalance
updated 3.8 years ago by
Michael Love
42k • written 3.8 years ago by
Vincent.C.
• 0
3 results • Page
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Comment: More regions in union when increasing DBA$config$mergeOverlap
by
Ian D.
▴ 70
Nudging my question. I could do with confirmation before proceeding with my current projects. Thank you.
Comment: Extremely small p-values using Limma for proteomic data
by
Robert Castelo
★ 3.3k
From the point of view of visualization, I find handy the fact that raw p-values give more resolution than adjusted ones, which allows one …
Comment: deseq2 results
by
ATpoint
★ 4.1k
> the results are not satisfactory to me Well, what is your question? The DESeq2 vignette covers how to do analysis, and some diagnostics…
Comment: Extremely small p-values using Limma for proteomic data
by
ATpoint
★ 4.1k
It's not an implementation problem I am discussing (it's trivial obviously) -- more that for most purposes the y-axis metric should be the …
Comment: Extremely small p-values using Limma for proteomic data
by
Robert Castelo
★ 3.3k
For visualization purposes you can draw an horizontal line at the p-value cutoff that meets the experiment-wide FDR cutoff. For instance, i…
Votes
Answer: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
Comment: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
Answer: minfi latest update for EPIC V2 chip
A: Error in DESeqDataSet : some values in assay are not integers
Answer: Cannot connect to ExperimentHub server
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Robert Castelo
★ 3.3k
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Gyan Prakash Mishra
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Gordon Smyth
50k
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WouterDeCoster
▴ 130
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Michael Love
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