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gagedata
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KEGG analysis for plasmodium
KEGG
gage
gageData
pathview
updated 3.1 years ago by
Luo Weijun
★ 1.6k • written 3.1 years ago by
MOHAMMAD
• 0
1
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2
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1.1k
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Can I create a gene set using GAGE?
gage
pathview
gageData
written 3.3 years ago by
Emilia
▴ 30
0
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0
replies
712
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Pathway Analysis using GAGE
gage
RNASeq
gageData
Pathways
2.0 years ago
OST
• 0
0
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0
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627
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Setting threshold with gage for gene set analysis
gage
gageData
3.1 years ago
jd348
• 0
4 results • Page
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Comment: Why p value inconsistent when using different number of pathway score?
by
Chris
• 0
Thanks ATpoint for you advice. Just don't understand the math behind the change in raw p value in this case. I think it is important to und…
Answer: Why p value inconsistent when using different number of pathway score?
by
ATpoint
★ 4.0k
Same answer as here: https://support.bioconductor.org/p/9157606/ Adding or removing data (samples, genes, pathways, observations...) chang…
Comment: The difference when using Limma compare between 3 conditions vs 2 conditions
by
Chris
• 0
Thanks Robert!
Comment: The difference when using Limma compare between 3 conditions vs 2 conditions
by
Robert Castelo
★ 3.2k
Hi, your `c2` object storing all the gene sets is probably a `list` object, where element names are the names of the pathways given by MSig…
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…
Votes
Answer: Why p value inconsistent when using different number of pathway score?
Comment: The difference when using Limma compare between 3 conditions vs 2 conditions
Installing/switching between versions of R/Rstudio/Bioconductor on personal machine (Linux | Ubuntu)
A: Docker container with bioconductor and devtools
Answer: OrgDb for maize
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