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TCGA CNV
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8.7k
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how to analyze TCGA CNV data
TCGA CNV
correlation between mRNA exprssion and CNV
updated 8.8 years ago by
spulido99
• 0 • written 9.7 years ago by
ycding
▴ 10
0
votes
4
replies
2.1k
views
Using cn.MOPs to estimate CNVs in tumors without reference normal
cn.mops
cnvtools
tcga cnv
updated 9.1 years ago by
Günter Klambauer
▴ 540 • written 9.1 years ago by
vakul.mohanty
▴ 20
27
votes
21
replies
24k
views
Mapping genome regions to gene symbols
tcga cnv
gene symbol
coordinate
updated 2.1 years ago by
James W. MacDonald
67k • written 9.6 years ago by
NS
▴ 60
3 results • Page
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Answer: RSubread output significantly different from bash Subread output
by
Gordon Smyth
52k
The difference (as ATpoint has correctly pointed out) is that Rsubread::featureCounts counts multi-mapping reads by default whereas the com…
Answer: Deseq2 Error in solve.default(qr.R(qrx)) : 'a' (1 x 0) must be square
by
Michael Love
43k
I would check the rank of your model matrix, and perhaps meet with a local statistician who can help you create an appropriate design matri…
Comment: sva: get a sv for RIN scores
by
gabriel.hoffman
▴ 170
Agreed. I'll add that with small sample size, a covariate can explain some fraction of expression variation even under the null.
Comment: RSubread output significantly different from bash Subread output
by
Aimee
• 0
Thank you! I will try rerunning with that parameter and see if it fixes the discrepancy! I'll report back. Update: This completely resolve…
Answer: RSubread output significantly different from bash Subread output
by
ATpoint
★ 4.6k
The R version counts multimappers (countMultiMappingReads is TRUE by default) while the command line version does not. It's beyond me why t…
Votes
Answer: RSubread output significantly different from bash Subread output
Answer: RSubread output significantly different from bash Subread output
Answer: How to annotate a limma Elist raw class object with an annotation file
Comment: How to annotate a limma Elist raw class object with an annotation file
QSEA- Extraction of Normalized methylation across the samples
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Michael Love
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Dario Strbenac
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ATpoint
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Gordon Smyth
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bhandary.8590
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