Showing : PureCN • reset
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Calculating tumour purity having only CNA data
PureCN CNA purity cancer
17 months ago JAcky • 0
1
vote
5
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1.2k
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Mutect version, matched normal and manual curation in PureCN
PureCN
18 months ago • updated 10 months ago Ken C • 0
1
vote
8
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1.3k
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PureCN: Copy Number of 7 issue
Pure PureCN
updated 2.0 years ago by ▴ 130 • written 2.0 years ago by • 0
1
vote
5
replies
1.1k
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PureCN C (integer segment copy number) in curated samples
PureC PureCN
updated 2.1 years ago by ▴ 130 • written 2.1 years ago by ▴ 10
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2
replies
842
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PureCN COSMIC VCF via PureCN.R - is there an option?
PureCN COSMIC
updated 2.2 years ago by ▴ 130 • written 2.3 years ago by ▴ 10
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1
reply
588
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PureCN performance of somatic/germline status prediction without matched normal?
SomaticMutation GermlineMutation PureCN
updated 2.3 years ago by ▴ 130 • written 2.3 years ago by ▴ 10
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3
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739
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Corrupt data in Sex column of .csv file
PureCN
2.6 years ago twtoal ▴ 10
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2
replies
996
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PureCN/ASCAT comparison and purity/ploidy of multi-regional sequencing data
PureCN ASCAT purity ploidy multi-regional sequencing
3.5 years ago twtoal ▴ 10
0
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3
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845
views
PureCN gene LOH very common, amp/del not
PureCN gene amplification deletion loh
updated 3.6 years ago by ▴ 130 • written 3.6 years ago by ▴ 10
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4
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831
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Why is PureCN LOH file missing some segments
purecn loh
3.8 years ago twtoal ▴ 10
0
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1
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656
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PureCN: Why is average coverage used for segmentation and not the denoised fragment counts?
PureCN CNV CNA segmentation calculateTangentNormal
updated 4.0 years ago by ▴ 130 • written 4.0 years ago by • 0
0
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2
replies
993
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PureCN version clashes at GitHub and Bioconductor
version PureCN
updated 4.0 years ago by ★ 6.2k • written 4.0 years ago by ▴ 10
0
votes
3
replies
779
views
callLOH output file NA values
PureCN NA values
updated 4.6 years ago by ▴ 130 • written 4.6 years ago by ▴ 10
0
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1
reply
854
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PureCN.R warning "duplicate keys in header will be forced to unique rownames"
PureCN
updated 4.6 years ago by ▴ 130 • written 4.6 years ago by ▴ 10
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1
reply
785
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Chromosome arm loss and --maxhomozygousloss default
Purecn maxhomozygousloss
5.0 years ago twtoal ▴ 10
2
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5
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2.3k
views
Issue with BiocParallel
purecn biocparallel
5.1 years ago milos-91 • 0
0
votes
1
reply
764
views
Copy ratio close to but not exactly 1
PureCN CopyRatio
updated 5.1 years ago by ▴ 130 • written 5.1 years ago by ▴ 10
0
votes
3
replies
943
views
Assigning DUP/DEL p-value to CNV segment
PureCN
5.2 years ago twtoal ▴ 10
0
votes
1
reply
898
views
Copy ratio threshold for calling actual CNV
PureCN copy-ratio threshold
updated 5.2 years ago by ▴ 130 • written 5.2 years ago by ▴ 10
0
votes
2
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804
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Mutation Burden file and manual curation
purecn mutation_burden manual_curation
5.2 years ago twtoal ▴ 10
0
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1
reply
863
views
PureCN Solution Heatmap values
PureCN heatmap likelihoods
5.2 years ago twtoal ▴ 10
0
votes
2
replies
986
views
CNV in Normal Samples?
PureCN Germline Normal CNV
updated 5.2 years ago by ▴ 130 • written 5.2 years ago by ▴ 10
1
vote
1
reply
769
views
PureCN recover optimum solution
PureCN Optimum_solution
updated 5.3 years ago by ▴ 130 • written 5.3 years ago by ▴ 10
0
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1
reply
641
views
PureCN PureCN.R --rds option recreate all output files?
PureCN --rds
updated 5.3 years ago by ▴ 130 • written 5.3 years ago by ▴ 10
1
vote
3
replies
900
views
PureCN Manual Curation .rds file
PureCN rds_file manual_curation
updated 5.3 years ago by ▴ 130 • written 5.3 years ago by ▴ 10
0
votes
4
replies
1.2k
views
PureCN optimum solution vs heat map
PureCN Solution Heatmap
updated 5.3 years ago by ▴ 130 • written 5.3 years ago by ▴ 10
0
votes
3
replies
1.7k
views
PureCN: Error in plot.window(...) : need finite 'ylim' values
PureCN
5.5 years ago • updated 5.3 years ago twtoal ▴ 10
0
votes
1
reply
1.0k
views
PureCN Error in xg[1, ] : incorrect number of dimensions
PureCN
5.5 years ago twtoal ▴ 10
0
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6
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1.5k
views
How can I improve somatic/germline status prediction without matched normal (PureCN)?
purecn
5.5 years ago skkujin • 0
0
votes
5
replies
1.5k
views
Is mean adjusted for purity?
PureCN mean ratio
updated 5.5 years ago by ▴ 130 • written 5.5 years ago by ▴ 10
3
votes
5
replies
1.4k
views
Understanding PureCN and its germline SNPs
PureCN germline SNP
updated 5.5 years ago by • 0 • written 5.7 years ago by ▴ 10
0
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1
reply
828
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Is C adjusted for purity?
PureCN Adjusted C
updated 5.6 years ago by ▴ 130 • written 5.6 years ago by ▴ 10
0
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9
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1.4k
views
Unable to find solution: low coverage
PureCN fatal error no solution
5.6 years ago twtoal ▴ 10
0
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2
replies
775
views
PureCN removemapq0 parameter
PureCN removemapq0
updated 5.6 years ago by ▴ 130 • written 5.6 years ago by ▴ 10
0
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4
replies
1.1k
views
Does Greater Depth Allow Low Purity To Work Well?
PureCN Purity Low Purity CNV
5.6 years ago twtoal ▴ 10
0
votes
6
replies
1.1k
views
Private Germline Count is mostly 0
PureCN private_germline mutation_burden
5.6 years ago twtoal ▴ 10
0
votes
2
replies
1.2k
views
PureCN use of VCF QUAL column for filtering when column is dot
PureCN VCF QUAL
updated 5.6 years ago by ▴ 130 • written 5.6 years ago by ▴ 10
0
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4
replies
1.0k
views
PureCN.R _variants.csv file prior.somatic and somatic variant count
PureCN Somatic Mutations
updated 5.6 years ago by ▴ 130 • written 5.6 years ago by ▴ 10
0
votes
2
replies
782
views
Dx.R somatic_ontarget column
PureCN
updated 5.6 years ago by ▴ 130 • written 5.6 years ago by ▴ 10
0
votes
1
reply
876
views
coverage QC file mean duplication and "mom" columns
PureCN coverage
updated 5.6 years ago by ▴ 130 • written 5.6 years ago by ▴ 10
1
vote
3
replies
839
views
PureCN Release Notes
PureCN Release
updated 5.6 years ago by 64k • written 5.6 years ago by ▴ 10
0
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1
reply
1.7k
views
VCF file non-SNP germline mutations
PureCN VCF SNP
updated 5.6 years ago by ▴ 130 • written 5.6 years ago by ▴ 10
0
votes
3
replies
869
views
PureCN warning: test.num.copy outside recommended range
PureCN Warning
updated 5.6 years ago by ▴ 130 • written 5.6 years ago by ▴ 10
0
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4
replies
1.2k
views
PureCN error: zero-length 'labels' specified
PureCN
5.6 years ago twtoal ▴ 10
0
votes
1
reply
678
views
PureCN Panel of Normals contents
PureCN
updated 5.6 years ago by ▴ 130 • written 5.6 years ago by ▴ 10
0
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2
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853
views
No CNAs or SNVs in results
PureCN
5.6 years ago twtoal ▴ 10
1
vote
1
reply
828
views
PureCN support for indels
PureCN indels
updated 5.7 years ago by ▴ 130 • written 5.7 years ago by ▴ 10
0
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9
replies
1.2k
views
errors in version 1.7.53
PureCN
updated 6.2 years ago by ▴ 130 • written 6.2 years ago by • 0
0
votes
1
reply
952
views
errors in Purecn callLOH
PureCN
updated 6.2 years ago by ▴ 130 • written 6.2 years ago by • 0
2
votes
3
replies
1.1k
views
PureCN can classify indel variants as germline vs. somatic ?
PureCN indel somatic germline
updated 6.5 years ago by ▴ 130 • written 6.5 years ago by • 0
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Comment: Correct the batch effect in methylation analysis in R by kyj2226 • 0
Thank you for your response Gordon :) I've already run the code below, just add batch to the limma linear model design <- model.matri…
Answer: Correct the batch effect in methylation analysis in R by Gordon Smyth 49k
You should not apply batch correction functions like harman before a limma analysis. Instead, just add `batch` to the limma linear model. …
Answer: Agilent Microarray Gene Oncology analysis gone wrong by Gordon Smyth 49k
Your use of `coef=1` is incorrect, for reasons explained in the limma User's Guide. If you had simply left `coef` at the default, then thin…
Comment: Normalised counts from RUVg in RUVSeq by Shaimaa Gamal • 0
Hello I was wondering if I should use ruv-corrected counts and ruv lib sizes to create a DGE object that can be used later for DE analysis …
Comment: enrichGOgradient color change by James W. MacDonald 64k
You could look at my answer and extrapolate from there.
Votes
Answer: Correct the batch effect in methylation analysis in R
Answer: enrichGOgradient color change
Answer: Filter genes by expression for voomLmFit
Answer: Filter genes by expression for voomLmFit
Answer: Filter genes by expression for voomLmFit
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