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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
7.7 years ago
sudhirjadhao2009
• 0
0
votes
4
replies
1.3k
views
Two color Nucleosomes ChIP-ChIP data analysis using Ringo package.
limma
ringo
starr
9.4 years ago
ashubiochem
• 0
0
votes
1
reply
1.6k
views
Ringo Plots Only Partially Made
Ringo
affy
tilingarray
plot
starr
9.5 years ago
bruce.moran
▴ 30
0
votes
1
reply
1.2k
views
Starr package: cmarrt.ma error
Starr
Starr
updated 10.8 years ago by
Julie Zhu
★ 4.3k • written 10.8 years ago by
Paul
▴ 10
0
votes
0
replies
1.1k
views
Starr package: cmarrt.ma error
Starr
Starr
10.8 years ago
Julie Zhu
★ 4.3k
0
votes
2
replies
1.2k
views
readCelFile function in Starr is crashing R
Starr
Starr
updated 13.2 years ago by
Kasper Daniel Hansen
★ 6.5k • written 13.2 years ago by
Guest User
★ 13k
0
votes
1
reply
938
views
help with Starr
GO
Starr
GO
Starr
updated 13.6 years ago by
Martin Morgan
25k • written 13.6 years ago by
Yongde Bao
▴ 170
0
votes
4
replies
1.5k
views
Reading GFF using Starr
Starr
Starr
updated 13.8 years ago by
zacher@lmb.uni-muenchen.de
▴ 50 • written 13.9 years ago by
Feseha Abebe-Akele
▴ 30
0
votes
1
reply
1.7k
views
tilingArray getting started questions
GO
Yeast
tilingArray
Starr
GO
Yeast
tilingArray
Starr
14.4 years ago
Noah Dowell
▴ 410
0
votes
3
replies
1.7k
views
ChIP-chip sequence bias not removed
Normalization
vsn
Starr
Normalization
vsn
Starr
updated 14.5 years ago by
zacher@lmb.uni-muenchen.de
▴ 50 • written 14.5 years ago by
Edwin Groot
▴ 230
0
votes
6
replies
1.8k
views
Question RE: getEnrichedGo in ChIPpeakAnno package
Yeast
ChIPpeakAnno
Starr
Yeast
ChIPpeakAnno
Starr
updated 14.6 years ago by
Julie Zhu
★ 4.3k • written 14.6 years ago by
Noah Dowell
▴ 410
0
votes
1
reply
1.0k
views
Starr - MAT normalization
Normalization
Starr
Normalization
Starr
updated 14.7 years ago by
Raphael Gottardo
▴ 40 • written 14.7 years ago by
Hans-Ulrich Klein
▴ 330
0
votes
1
reply
1.0k
views
Ringo/Starr getProfiles function
Annotation
Starr
Annotation
Starr
updated 15.1 years ago by
zacher@lmb.uni-muenchen.de
▴ 50 • written 15.1 years ago by
Noah Dowell
▴ 410
0
votes
1
reply
1.0k
views
Ringo/Starr getProfiles function
biomaRt
Ringo
Starr
biomaRt
Ringo
Starr
updated 15.1 years ago by
Wolfgang Huber
★ 13k • written 15.1 years ago by
Noah Dowell
▴ 410
0
votes
1
reply
913
views
Please Help with Starr Package
Normalization
Starr
Normalization
Starr
updated 15.1 years ago by
Martin Morgan
25k • written 15.1 years ago by
Noah Dowell
▴ 410
0
votes
1
reply
1.4k
views
Help with Oligo Package: Extracting and Graphing
Transcription
Normalization
Yeast
probe
affy
graph
tilingArray
oligo
pdInfoBuilder
Starr
updated 15.2 years ago by
Tobias Straub
▴ 430 • written 15.2 years ago by
Noah Dowell
▴ 410
16 results • Page
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Replies
Comment: Different annotation packages (org.Mm.eg.db, EnsDb.Mmusculus.v79, BiomaRt) retu
by
ATpoint
★ 4.6k
Given that the annotation versions were the same the results *should* be identical, but for such a simple task as making a tx2gene why not …
Answer: Differential variability modelling with vst() expression
by
Gordon Smyth
52k
See Phipson, B., Oshlack, A. DiffVar: a new method for detecting differential variability with application to methylation in cancer and …
Answer: Differential variability modelling with vst() expression
by
Michael Love
43k
Looking at differential variance across groups, where you regress out orthogonal nuisance factors from VST data, seems correct and would po…
Answer: Installation error for Rsamtools.
by
James W. MacDonald
67k
It's already installed. Note the warning: ``` Warning message: package(s) not installed when version(s) same as or greater than curren…
Comment: Different annotation packages (org.Mm.eg.db, EnsDb.Mmusculus.v79, BiomaRt) retu
by
Nicholas
• 0
Just an update on this: I tried ```tximport``` with ```tx2gene``` objects from the three annotation packages and from the GTF file itself. …
Votes
Comment: Different annotation packages (org.Mm.eg.db, EnsDb.Mmusculus.v79, BiomaRt) retu
Answer: Different annotation packages (org.Mm.eg.db, EnsDb.Mmusculus.v79, BiomaRt) retu
Comment: Why did PCA plots look exactly the same after adjusting for batch covariate in D
Why did PCA plots look exactly the same after adjusting for batch covariate in DESeq2 design?
A: Trajectory analysis for single cell sequencing
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