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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
7.0 years ago
sudhirjadhao2009
• 0
0
votes
4
replies
1.2k
views
Two color Nucleosomes ChIP-ChIP data analysis using Ringo package.
limma
ringo
starr
8.7 years ago
ashubiochem
• 0
0
votes
1
reply
1.4k
views
Ringo Plots Only Partially Made
Ringo
affy
tilingarray
plot
starr
8.8 years ago
bruce.moran
▴ 30
0
votes
1
reply
1.0k
views
Starr package: cmarrt.ma error
Starr
Starr
updated 10.1 years ago by
Julie Zhu
★ 4.3k • written 10.1 years ago by
Paul
▴ 10
0
votes
0
replies
955
views
Starr package: cmarrt.ma error
Starr
Starr
10.1 years ago
Julie Zhu
★ 4.3k
0
votes
2
replies
1.1k
views
readCelFile function in Starr is crashing R
Starr
Starr
updated 12.5 years ago by
Kasper Daniel Hansen
★ 6.5k • written 12.5 years ago by
Guest User
★ 13k
0
votes
1
reply
829
views
help with Starr
GO
Starr
GO
Starr
updated 12.9 years ago by
Martin Morgan
25k • written 12.9 years ago by
Yongde Bao
▴ 170
0
votes
4
replies
1.3k
views
Reading GFF using Starr
Starr
Starr
updated 13.2 years ago by
zacher@lmb.uni-muenchen.de
▴ 50 • written 13.2 years ago by
Feseha Abebe-Akele
▴ 30
0
votes
1
reply
1.6k
views
tilingArray getting started questions
GO
Yeast
tilingArray
Starr
GO
Yeast
tilingArray
Starr
13.7 years ago
Noah Dowell
▴ 410
0
votes
3
replies
1.5k
views
ChIP-chip sequence bias not removed
Normalization
vsn
Starr
Normalization
vsn
Starr
updated 13.8 years ago by
zacher@lmb.uni-muenchen.de
▴ 50 • written 13.8 years ago by
Edwin Groot
▴ 230
0
votes
6
replies
1.6k
views
Question RE: getEnrichedGo in ChIPpeakAnno package
Yeast
ChIPpeakAnno
Starr
Yeast
ChIPpeakAnno
Starr
updated 13.9 years ago by
Julie Zhu
★ 4.3k • written 13.9 years ago by
Noah Dowell
▴ 410
0
votes
1
reply
901
views
Starr - MAT normalization
Normalization
Starr
Normalization
Starr
updated 14.0 years ago by
Raphael Gottardo
▴ 40 • written 14.0 years ago by
Hans-Ulrich Klein
▴ 330
0
votes
1
reply
892
views
Ringo/Starr getProfiles function
Annotation
Starr
Annotation
Starr
updated 14.4 years ago by
zacher@lmb.uni-muenchen.de
▴ 50 • written 14.4 years ago by
Noah Dowell
▴ 410
0
votes
1
reply
934
views
Ringo/Starr getProfiles function
biomaRt
Ringo
Starr
biomaRt
Ringo
Starr
updated 14.4 years ago by
Wolfgang Huber
★ 13k • written 14.4 years ago by
Noah Dowell
▴ 410
0
votes
1
reply
811
views
Please Help with Starr Package
Normalization
Starr
Normalization
Starr
updated 14.4 years ago by
Martin Morgan
25k • written 14.4 years ago by
Noah Dowell
▴ 410
0
votes
1
reply
1.2k
views
Help with Oligo Package: Extracting and Graphing
Transcription
Normalization
Yeast
probe
affy
graph
tilingArray
oligo
pdInfoBuilder
Starr
updated 14.5 years ago by
Tobias Straub
▴ 430 • written 14.5 years ago by
Noah Dowell
▴ 410
16 results • Page
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Answer: How to use bootRanges to bootstrap small RNA loci (nullranges package)
by
Poonam
• 0
Hi Michael, I think there is something wrong with the generation of nullranges. I was working with small RNA and methylation overlaps. …
Answer: Once again a "Model matrix not full rank"
by
swbarnes2
★ 1.3k
Replicate numbers, like the 1 in control_1 are fine in sample names, but never add them to anything else in colData. From the computer's p…
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I'll add a little bit of general advice to James' answer. You seem to have the misunderstanding that you can change the design matrix but …
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It is true that goseq isn't available for Bioc 3.19 (as at 4 May 2024). In the meantime, you could consider using the goana() and kegga() …
Answer: limma Intercept vs No-intercept models completely changing DMR results?
by
James W. MacDonald
65k
This part: ``` design_intercept <- model.matrix(~Alt+Sex+Age+PC1, data=targets_Sherpa) colnames(design_intercept) <- c("AltSHP_LA","Al…
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Answer: Why does GSEA on edgeR results for randomized samples give highly significant p-
Answer: limma Intercept vs No-intercept models completely changing DMR results?
Answer: CombineArrays for EPIC and EPIC V2
Answer: Too many significant genes when integrating gtex and tcga
Comment: Too many significant genes when integrating gtex and tcga
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