Showing : cn.MOPS • reset
2
votes
5
replies
1.4k
views
Error in referencecn.mops() for paired exome sequencing (normal/tumor)
cn.mops
updated 8.2 years ago by ▴ 540 • written 8.3 years ago by ▴ 10
2
votes
6
replies
2.6k
views
Cn.mops error: Error in if (sum(rds.counts) == 0) { : missing value where TRUE/FALSE needed
software error cn.mops
updated 8 weeks ago by • 0 • written 6.3 years ago by ▴ 10
1
vote
7
replies
2.3k
views
Extracting CNV data from CNVDetectionResult
cn.mops
updated 8.4 years ago by ▴ 540 • written 8.8 years ago by • 0
0
votes
5
replies
1.4k
views
p or fdr values
cn.mops
8.7 years ago billnjcn • 0
3
votes
12
replies
2.4k
views
Error installing cn.mops and Rsamtools in R 3.1.3
rsamtools cn.mops installation
9.1 years ago Spollen, William G. ▴ 30
0
votes
4
replies
1.4k
views
No CNVs detected. Try changing "normalization", "priorImpact" or "thresholds".
No CNVs detected. Try changing "normalization" "priorImpact" or "thresholds". cn.mops
updated 7.6 years ago by ▴ 540 • written 7.6 years ago by • 0
0
votes
18
replies
4.5k
views
cn.MOPs: Error in value[[3L]](cond) :
cn.mops
updated 5.8 years ago by ▴ 540 • written 5.8 years ago by • 0
0
votes
3
replies
1.8k
views
cn.mops CNV calling for multiple samples
cn.mops
updated 8.3 years ago by ▴ 540 • written 8.4 years ago by • 0
0
votes
5
replies
1.4k
views
Complete chromosome losses and polyploidies
cn.mops polyploidy
8.5 years ago mikko.arvas • 0
5
votes
9
replies
1.8k
views
reduce function after combining 2 GRanges objects from cn.mops output
GRanges cn.mops
updated 6.9 years ago by ★ 11k • written 6.9 years ago by ▴ 110
0
votes
3
replies
945
views
tumor vs control: multiple samples
cn.mops
5.4 years ago • updated 5.3 years ago DannyM • 0
0
votes
2
replies
1.1k
views
getReadCountsFromBAM and paired-end reads
cn.mops
6.9 years ago Alexandre Kuhn ▴ 20
5
votes
7
replies
1.5k
views
about the runs with cn.mops
cn.mops referencecn.mops
6.7 years ago Bogdan ▴ 670
2
votes
8
replies
2.4k
views
Copy Number Variation in the cn.mops Package
cn.mops cnv cnvtools
updated 8.8 years ago by 25k • written 8.8 years ago by • 0
2
votes
2
replies
1.2k
views
Save plot as png in cn.MOPS
cn.mops
8.3 years ago ashkot09 • 0
4
votes
3
replies
1.3k
views
parameter "refSeqName" in function "getReadCountsFromBAM"
cn.mops
updated 7.2 years ago by ▴ 540 • written 7.7 years ago by • 0
0
votes
4
replies
1.3k
views
cn.mops encounter negative width problem
cn.mops referencecn.mops
updated 7.0 years ago by ▴ 540 • written 7.0 years ago by • 0
4
votes
2
replies
1.4k
views
using cn.MOPS on WES data GERMLINE-TUMOR
cn.mops
6.9 years ago Bogdan ▴ 670
0
votes
1
reply
848
views
Input (X) data type is not numeric if read from GRanges obj
cn.mops
updated 7.4 years ago by ▴ 540 • written 7.4 years ago by • 0
4
votes
9
replies
2.4k
views
How to use cn.mops to detect CNVs from Targeted DNA Sequencing data?
cn.mops cnv targeted sequencing
updated 7.3 years ago by ▴ 540 • written 7.3 years ago by ▴ 20
0
votes
4
replies
1.4k
views
Call CNV in population with large depth variance
cn.mops
updated 7.3 years ago by ▴ 540 • written 7.3 years ago by • 0
3
votes
5
replies
1.5k
views
R code for cn.mops
cn.mops
updated 13 months ago by • 0 • written 7.2 years ago by ▴ 670
3
votes
1
reply
1.2k
views
R code for cn.mops -- if a chromosome does not have CNV ?
cn.mops referencecn.mops
updated 7.0 years ago by ▴ 540 • written 7.2 years ago by ▴ 670
0
votes
1
reply
1.1k
views
cn.mops returning only "NA" as copy number
cn.mops
updated 7.2 years ago by ▴ 540 • written 7.2 years ago by • 0
1
vote
1
reply
970
views
which cn.mops function should I use
cn.mops
updated 7.0 years ago by ▴ 540 • written 7.0 years ago by • 0
0
votes
2
replies
1.3k
views
Conflict in cnvr and cnvs result from cn.mops
cn.mops
updated 6.9 years ago by ▴ 540 • written 7.0 years ago by • 0
2
votes
1
reply
1.0k
views
How to combine CNVDetectionResult objects in cn.mops package
cn.mops
updated 6.9 years ago by ▴ 540 • written 6.9 years ago by ▴ 110
0
votes
1
reply
1.0k
views
getReadCountsFromBAM including bed information
cn.mops bed files getReadCountsFromBAM
6.8 years ago Pau Marc Muñoz Torres ▴ 20
1
vote
2
replies
1.6k
views
cn.MOPS - reporting log normalized read counts as table
cn.mops log normalized counts table
updated 6.8 years ago by ▴ 540 • written 6.8 years ago by • 0
0
votes
4
replies
1.3k
views
Is cn.mops can be used for detecting CNV for targeted sequencing of 8M region
cn.mops
updated 6.4 years ago by ▴ 540 • written 6.4 years ago by • 0
0
votes
2
replies
1.5k
views
cn.MOPs issue with "Error in if (all(segMedianT == 0))"
cn.mops cnv
updated 6.4 years ago by ▴ 540 • written 6.4 years ago by ▴ 20
0
votes
5
replies
1.5k
views
Error when use getSegmentReadCountsFromBAM
targeted sequencing cn.mops
6.3 years ago jinxinhao1988 • 0
0
votes
1
reply
963
views
Error with plotting with target sequencing data
cn.mops
updated 6.2 years ago by ▴ 540 • written 6.2 years ago by • 0
0
votes
1
reply
1.3k
views
Detection copy number variations with cn.MOPS package
Coverage cn.mops Coverage cn.mops
updated 11.4 years ago by ▴ 540 • written 11.4 years ago by ▴ 50
0
votes
2
replies
1.7k
views
cn.mops: copy number for low-coverage bam files?
Sequencing Coverage cn.mops Sequencing Coverage cn.mops
updated 11.0 years ago by ▴ 540 • written 11.0 years ago by ▴ 750
1
vote
1
reply
1.1k
views
copy number segment calling with cn.mop when just one sample?
cn.mops cn.mops
updated 8.8 years ago by ▴ 540 • written 10.9 years ago by ▴ 750
0
votes
1
reply
1.4k
views
Negative Width error in cn.mops
cn.mops cn.mops
updated 8.8 years ago by ▴ 540 • written 10.6 years ago by ▴ 10
0
votes
1
reply
984
views
error in calculate integer copy numbers. bug?
cn.mops cn.mops
updated 10.3 years ago by ▴ 540 • written 10.3 years ago by ★ 13k
0
votes
1
reply
987
views
CNV detection using cn.farms for non-affymetrix arrays (custom oligonucleotide arrays)
Sequencing Microarray probe cn.mops Sequencing Microarray probe cn.mops
updated 10.1 years ago by ▴ 210 • written 10.1 years ago by ★ 13k
2
votes
2
replies
1.8k
views
Adjusting the defaults in the cn.MOPs Package
cn.mops cnv cnvtools
updated 8.8 years ago by ▴ 540 • written 8.8 years ago by • 0
1
vote
3
replies
1.7k
views
"Some normalization factors are zero" error on cn.mops
cn.mops
updated 8.8 years ago by ▴ 540 • written 8.8 years ago by ▴ 590
0
votes
1
reply
970
views
Unpaired CNV Exome
cn.mops
updated 8.8 years ago by ▴ 540 • written 8.8 years ago by • 0
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 ▴ 540 • written 8.5 years ago by ▴ 20
2
votes
6
replies
1.8k
views
refSeqName issue in cn.MOPS
CNV cn.mops
updated 8.3 years ago by ▴ 540 • written 8.3 years ago by • 0
0
votes
1
reply
1.0k
views
cn.MOPS output file
cn.mops
updated 8.3 years ago by ▴ 540 • written 8.3 years ago by • 0
1
vote
4
replies
1.6k
views
Detect CNVs in target sample
CNV cn.mops
updated 8.3 years ago by ▴ 540 • written 8.3 years ago by • 0
0
votes
1
reply
876
views
problems on the CNV detection by cn.mops using multiply WGS data
cn.mops
updated 7.9 years ago by ▴ 540 • written 7.9 years ago by • 0
0
votes
2
replies
906
views
why there are multiple calls to cnmops C function?
cn.mops
updated 7.7 years ago by ▴ 540 • written 7.7 years ago by • 0
1
vote
1
reply
867
views
Suggestion: type of ExpLogFoldChange (sini)
cn.mops
updated 7.6 years ago by ▴ 540 • written 7.6 years ago by • 0
0
votes
2
replies
1.1k
views
about cn.MOPS: paired vs unpaired
cn.mops
updated 7.5 years ago by ▴ 540 • written 7.5 years ago by ▴ 670
50 results • Page 1 of 1
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Comment: Method to find pathways different between 2 groups by Gordon Smyth 50k
sigPathway is another method that does not account for inter-gene correlation and which gives inflated significance, as we showed in our 20…
Answer: error in limma , contrast.matrix Number of rows of contrast matrix must match nu by James W. MacDonald 65k
I doubt you have that many contrasts. I think that is probably the number of rows. What does `dim(fit)` return (and `head(fit$coef)`)?
Answer: Extremely small p-values using Limma for proteomic data by James W. MacDonald 65k
If you fit a cell means model (without an intercept), you will have to construct contrasts using `makeContrasts` and fit them using `contra…
Comment: Memory errors using read.bismark? by Juan Higareda • 0
Thanks a lot Peter, We solved the problem, IT had implemented a policy of RAM usage that started a conflict with any RAM-hungry process, m…
Answer: meffil.snp.concordance by James W. MacDonald 65k
This support site is meant to help people with technical questions about Bioconductor packages. The `meffil` package is not Bioconductor, n…
Votes
Answer: error in limma , contrast.matrix Number of rows of contrast matrix must match nu
Answer: Extremely small p-values using Limma for proteomic data
Answer: How to save the DEXSeq results
Answer: minfi support of illumina Infinium methylationEPIC v2.0
Comment: minfi support of illumina Infinium methylationEPIC v2.0
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