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TCGA CNV
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8.4k
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how to analyze TCGA CNV data
TCGA CNV
correlation between mRNA exprssion and CNV
updated 8.2 years ago by
spulido99
• 0 • written 9.1 years ago by
ycding
▴ 10
0
votes
4
replies
1.9k
views
Using cn.MOPs to estimate CNVs in tumors without reference normal
cn.mops
cnvtools
tcga cnv
updated 8.5 years ago by
Günter Klambauer
▴ 540 • written 8.5 years ago by
vakul.mohanty
▴ 20
27
votes
21
replies
23k
views
Mapping genome regions to gene symbols
tcga cnv
gene symbol
coordinate
updated 18 months ago by
James W. MacDonald
65k • written 9.0 years ago by
NS
▴ 60
3 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…
Answer: limma Intercept vs No-intercept models completely changing DMR results?
by
Gordon Smyth
50k
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 …
Answer: package goseq seems to be not available on the latest version of R
by
Gordon Smyth
50k
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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