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starr
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how to analyse chip-chip on normalized data without bpmap file or how to select bpmap file for your data(data downloaded from NCBI geo)
starr
chip-chip
8.7 years ago
sudhirjadhao2009
• 0
0
votes
4
replies
1.6k
views
Two color Nucleosomes ChIP-ChIP data analysis using Ringo package.
limma
ringo
starr
10.4 years ago
ashubiochem
• 0
0
votes
1
reply
1.8k
views
Ringo Plots Only Partially Made
Ringo
affy
tilingarray
plot
starr
10.5 years ago
bruce.moran
▴ 30
0
votes
1
reply
1.3k
views
Starr package: cmarrt.ma error
Starr
Starr
updated 11.8 years ago by
Julie Zhu
★ 4.3k • written 11.8 years ago by
Paul
▴ 10
0
votes
0
replies
1.2k
views
Starr package: cmarrt.ma error
Starr
Starr
11.8 years ago
Julie Zhu
★ 4.3k
0
votes
2
replies
1.5k
views
readCelFile function in Starr is crashing R
Starr
Starr
updated 14.2 years ago by
Kasper Daniel Hansen
★ 6.5k • written 14.2 years ago by
Guest User
★ 13k
0
votes
1
reply
1.1k
views
help with Starr
GO
Starr
GO
Starr
updated 14.6 years ago by
Martin Morgan
25k • written 14.6 years ago by
Yongde Bao
▴ 170
0
votes
4
replies
1.7k
views
Reading GFF using Starr
Starr
Starr
updated 14.9 years ago by
zacher@lmb.uni-muenchen.de
▴ 50 • written 14.9 years ago by
Feseha Abebe-Akele
▴ 30
0
votes
1
reply
1.9k
views
tilingArray getting started questions
GO
Yeast
tilingArray
Starr
GO
Yeast
tilingArray
Starr
15.4 years ago
Noah Dowell
▴ 410
0
votes
3
replies
2.0k
views
ChIP-chip sequence bias not removed
Normalization
vsn
Starr
Normalization
vsn
Starr
updated 15.5 years ago by
zacher@lmb.uni-muenchen.de
▴ 50 • written 15.5 years ago by
Edwin Groot
▴ 230
0
votes
6
replies
2.2k
views
Question RE: getEnrichedGo in ChIPpeakAnno package
Yeast
ChIPpeakAnno
Starr
Yeast
ChIPpeakAnno
Starr
updated 15.6 years ago by
Julie Zhu
★ 4.3k • written 15.6 years ago by
Noah Dowell
▴ 410
0
votes
1
reply
1.2k
views
Starr - MAT normalization
Normalization
Starr
Normalization
Starr
updated 15.7 years ago by
Raphael Gottardo
▴ 40 • written 15.7 years ago by
Hans-Ulrich Klein
▴ 330
0
votes
1
reply
1.2k
views
Ringo/Starr getProfiles function
Annotation
Starr
Annotation
Starr
updated 16.1 years ago by
zacher@lmb.uni-muenchen.de
▴ 50 • written 16.1 years ago by
Noah Dowell
▴ 410
0
votes
1
reply
1.2k
views
Ringo/Starr getProfiles function
biomaRt
Ringo
Starr
biomaRt
Ringo
Starr
updated 16.1 years ago by
Wolfgang Huber
★ 13k • written 16.1 years ago by
Noah Dowell
▴ 410
0
votes
1
reply
1.1k
views
Please Help with Starr Package
Normalization
Starr
Normalization
Starr
updated 16.1 years ago by
Martin Morgan
25k • written 16.1 years ago by
Noah Dowell
▴ 410
0
votes
1
reply
1.6k
views
Help with Oligo Package: Extracting and Graphing
Transcription
Normalization
Yeast
probe
affy
graph
tilingArray
oligo
pdInfoBuilder
Starr
updated 16.2 years ago by
Tobias Straub
▴ 430 • written 16.2 years ago by
Noah Dowell
▴ 410
16 results • Page
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Comment: Question about the filterByExpr function inputs in edgeR
by
Gordon Smyth
53k
Regarding edgeR v4 filtering, I didn't mention anything about a minimum count of 10 but rather said "a positive count". So a minimalistic f…
Comment: limpa-blank normalization and Spectronaut's PTM stoichiometry
by
JKim
• 0
Hi Emily, He left some comments regarding normalization. Here is the relevant quote: > The EList object produced by dpcQuant(), containi…
Comment: Joining different datasets and analyzing using the group-specific condition effe
by
James W. MacDonald
68k
Yes, making a group factor simplifies things, and you will need a new column for disease subject to avoid having a design that is not full …
Comment: Question about the filterByExpr function inputs in edgeR
by
mohammedtoufiq91
▴ 10
@gordonsmyth Yes, Gender is more a nuisance factor in our experiment, and our primary interest is to compare groups. I will just use filter…
Comment: Joining different datasets and analyzing using the group-specific condition effe
by
jason.chai
• 0
Thank you very much. I had read that and wondered if I used the recommendation in DESeq vignette, I would lose the pairing between groups? …
Votes
Answer: Question about the filterByExpr function inputs in edgeR
Answer: Question about the filterByExpr function inputs in edgeR
A: DESeq2: What is the unit of DESeq2 normalized read count (VST)? Is it tag per mi
Answer: Clarification on counting in Rsubread (featureCounts)
Comment: Clarification on counting in Rsubread (featureCounts)
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