Showing : dnacopy • reset
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116
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DNAcopy segment function not reproducible even when setting seed
DNAcopy
6 weeks ago BID • 0
0
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0
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626
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NAs in tabular output from DNAcopy
Bioconductor DNAcopy
8 months ago NewtoBioconductor • 0
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0
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489
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do DNAcopy do copy number segmentation need separate between tumor samples and mormal samples
DNAcopy
2.4 years ago xingyu • 0
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1
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2.0k
views
BiocManager::install("DNAcopy") failed to install in r
DNAcopy R
updated 2.6 years ago by ★ 6.5k • written 2.6 years ago by • 0
0
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11
replies
1.5k
views
Create `Copy Number Array' Data Object error
DNAcopy
3.4 years ago El • 0
0
votes
3
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1.7k
views
"genomdat must be numeric"error in DNAcopy Package (Solved)
DNAcopy Varscan
updated 3.4 years ago by • 0 • written 6.2 years ago by • 0
0
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0
replies
630
views
don't get an output of wigtoRangedData's function HMMcopy Package for detect CNV
HMMcopy DNAcopy
3.5 years ago El • 0
2
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3
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1.5k
views
Doubt about WL in cn.mops
dnacopy dnaseq genomic cn.mops cnv
updated 5.8 years ago by ▴ 540 • written 5.8 years ago by • 0
0
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1
reply
2.4k
views
change plot title in DNAcopy multiple plot.type="s"
DNAcopy
updated 6.5 years ago by ▴ 680 • written 6.5 years ago by ▴ 60
0
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0
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787
views
plot multiple chromosomes from plot.type="c" to PDF files automatically in RStudio (RMD document)
dnacopy
6.5 years ago Stephane Plaisance | VIB | ▴ 60
0
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3
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1.4k
views
wrong output of DNAcopy::segment() for chr. with empty copy number data
DNAcopy dnacopy
6.7 years ago Alexandre Kuhn ▴ 20
0
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3
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1.5k
views
Analysing TCGA Level 3 Copy Number Data Location of markers in the genome
TCGA Cancer dnacopy segmentation
updated 6.8 years ago by ▴ 130 • written 6.8 years ago by • 0
1
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2
replies
1.3k
views
DNAcopy segmentation issue: min.width argument not working?
dnacopy segmentation CBS
updated 7.2 years ago by ▴ 30 • written 7.2 years ago by ▴ 10
2
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4
replies
2.3k
views
Visualizing CopywriteR's segmentation output in IGV
copywriter dnacopy
updated 8.2 years ago by ▴ 170 • written 8.2 years ago by • 0
0
votes
2
replies
1.1k
views
could not find function "DNAcopy"
dnacopy
updated 8.2 years ago by 25k • written 8.2 years ago by • 0
0
votes
1
reply
1.5k
views
CNAnorm ploidy help
CNAnorm DNAcopy
updated 8.4 years ago by • 0 • written 8.4 years ago by ▴ 40
0
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0
replies
920
views
Get data frame of CNV calls from Seglist object
seglist snapcgh dnacopy
8.7 years ago Cian Murphy ▴ 40
0
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1
reply
1.3k
views
"genomdat must be numeric" error form DNACopy package
software error dnacopy crlmm
updated 8.9 years ago by 65k • written 8.9 years ago by • 0
0
votes
0
replies
1.4k
views
DNAcopy default settings and SNP6.0 arrays
SNP DNAcopy SNP6.0 CNV
9.3 years ago giovanni.dario • 0
1
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1
reply
1.2k
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Installation of DNAcopy was absolutly done in R2.15?
installation dnacopy
9.4 years ago vov-x • 0
0
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4
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1.8k
views
DNACopy Question what is passed to the maploc argument.
DNAcopy DNAcopy
updated 9.8 years ago by ★ 6.8k • written 9.8 years ago by ▴ 30
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0
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1.0k
views
DNA Copy CNA function , what do you pass to maploc argument?
DNAcopy DNAcopy
9.8 years ago Nikolas Balanis ▴ 30
0
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3
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3.6k
views
Error installing impute package
GUI impute DNAcopy GUI impute DNAcopy
updated 9.9 years ago by ★ 8.2k • written 9.9 years ago by ▴ 80
0
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0
replies
1.2k
views
CGHCall problems
aCGH probe DNAcopy aCGH CGHcall aCGH probe DNAcopy aCGH CGHcall
10.8 years ago Guest User ★ 13k
0
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0
replies
1.2k
views
readPositionalInfo in snapCGH for preparing CNA files for DNAcopy
aCGH DNAcopy aCGH snapCGH aCGH DNAcopy aCGH snapCGH
10.8 years ago Guest User ★ 13k
0
votes
1
reply
1.6k
views
Error in sort(abs(diff(genomdat)))[1:n.keep]
DNAcopy DNAcopy
updated 11.0 years ago by ▴ 40 • written 11.0 years ago by ★ 13k
0
votes
3
replies
1.4k
views
Error installing (some) Bioconductor packages on Mac OSX under R-3.0.0?
GUI impute DNAcopy GUI impute DNAcopy
updated 11.1 years ago by ★ 8.2k • written 11.1 years ago by ★ 3.0k
0
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1
reply
1.4k
views
Can we use DNAcopy to analyse Copy Number Viaration using next generation sequencing data generated by eigher Ion PGM or Illumina MiSeq
Sequencing DNAcopy Sequencing DNAcopy
updated 11.3 years ago by ▴ 210 • written 11.3 years ago by ★ 13k
0
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5
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1.7k
views
bioconductor on EMR / mapreduce
DNAcopy DNAcopy
updated 11.6 years ago by ★ 8.2k • written 11.6 years ago by ▴ 70
0
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1
reply
1.6k
views
DNAcopy for CNV in SNP Affy 6.0
SNP affy DNAcopy SNP affy DNAcopy
12.1 years ago Ekta Jain ▴ 370
0
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1
reply
1.1k
views
DNAcopy for CNV in SNP Affy 6.0
DNAcopy DNAcopy
updated 12.1 years ago by 6.7k • written 12.1 years ago by ▴ 370
0
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0
replies
1.1k
views
aCGH segmentation with DNAcopy
aCGH probe DNAcopy aCGH aCGH probe DNAcopy aCGH
12.2 years ago Emilie Lalonde ▴ 10
0
votes
1
reply
1.3k
views
CNTools error message
CGH probe DNAcopy CGH probe DNAcopy
updated 12.3 years ago by 25k • written 12.3 years ago by ▴ 280
0
votes
2
replies
1.2k
views
questions on cghMCR package
DNAcopy cghMCR DNAcopy cghMCR
updated 12.3 years ago by 25k • written 12.3 years ago by ▴ 280
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0
replies
1.0k
views
Fwd: seeking help on cghMCR pleeeease
DNAcopy cghMCR DNAcopy cghMCR
12.4 years ago nac ▴ 280
0
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0
replies
972
views
seeking help on cghMCR pleeeease
DNAcopy cghMCR DNAcopy cghMCR
12.4 years ago nac ▴ 280
0
votes
0
replies
1.0k
views
Help on cghMCR units of gapAllowed
DNAcopy cghMCR DNAcopy cghMCR
12.4 years ago nac ▴ 280
0
votes
2
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1.6k
views
Tuning segment() in DNAcopy package to get more segments on each chromosome
DNAcopy UNDO DNAcopy UNDO
updated 12.5 years ago by 21k • written 12.5 years ago by ▴ 110
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0
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1.2k
views
cghMCR package:Is it possible to find MCR by not usingDNAcopy object?
PROcess DNAcopy cghMCR PROcess DNAcopy cghMCR
12.6 years ago viritha kaza ▴ 580
0
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1
reply
1.3k
views
cghMCR package:Is it possible to find MCR by not using DNAcopy object?
DNAcopy cghMCR DNAcopy cghMCR
updated 12.6 years ago by ▴ 20 • written 12.6 years ago by ▴ 580
0
votes
1
reply
1.0k
views
DNAcopy segment() Infinite Loop
DNAcopy DNAcopy
updated 12.9 years ago by ▴ 40 • written 12.9 years ago by ★ 1.5k
2
votes
1
reply
1.5k
views
DNAcopy
DNAcopy copynumber DNAcopy copynumber
updated 12.9 years ago by 21k • written 12.9 years ago by ▴ 140
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2
replies
1.3k
views
DNA copy ploting function
probe DNAcopy probe DNAcopy
12.9 years ago nac ▴ 280
0
votes
1
reply
895
views
[Fwd: Problem with DNAcopy plot function ??]
DNAcopy DNAcopy
updated 13.0 years ago by ★ 13k • written 13.0 years ago by ▴ 280
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0
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769
views
[Fwd: Problem with DNAcopy plot function ??]
DNAcopy DNAcopy
13.0 years ago nac ▴ 280
0
votes
0
replies
841
views
How to get defenitive Amp/del/nochange using DNAcopy package?
graph DNAcopy graph DNAcopy
13.0 years ago Chiho Kwon ▴ 10
0
votes
1
reply
910
views
DNAcopy installation error
DNAcopy DNAcopy
updated 14.2 years ago by 25k • written 14.2 years ago by ▴ 10
0
votes
0
replies
1.1k
views
DNAcopy
aCGH impute DNAcopy aCGH snapCGH CGHcall aCGH impute DNAcopy aCGH snapCGH CGHcall
14.3 years ago Daniel Rico ▴ 110
0
votes
0
replies
952
views
DNAcopy
aCGH DNAcopy aCGH aCGH DNAcopy aCGH
14.3 years ago Anguraj Sadanandam ▴ 10
0
votes
2
replies
1.1k
views
Reproducibility of DNAcopy segmentation
DNAcopy DNAcopy
updated 14.3 years ago by 21k • written 14.3 years ago by ▴ 20
50 results • Page 1 of 1
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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. That is because goseq depends on txbmaker, which is itself not yet available for Bioc…
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…
Comment: CombineArrays for EPIC and EPIC V2 by Kim • 0
Thank you Tim, this is a great help in getting me started!
Votes
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
A: Print Differentially Expressed Exons From Dexseq Results
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