Showing : bumphunter • reset
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424
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minfi - bumphunter value problem
bumphunter minfiData minfi bumphun
updated 5 months ago by 67k • written 5 months ago by • 0
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3
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1.0k
views
minfi bumphunter - probe IDs
minfi bumphunter
updated 14 months ago by ▴ 780 • written 14 months ago by • 0
0
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1
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867
views
specifying comparison of interest in the minfi Bumhunter function
limma bumphunter methylationArrayAnalysis minfi
updated 21 months ago by 67k • written 21 months ago by • 0
0
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0
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910
views
Error: 'bumphunter()' only supports matrix-backed minfi objects.
bumphunter minfi genomi
2.5 years ago runye • 0
0
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0
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895
views
Does bump hunter support Infinium Mouse Methylation BeadChip Array data?
bumphunter
2.8 years ago ZHAOHUI • 0
0
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9
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3.7k
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clarification about bumphunter value output
minfi bumphunter
updated 19 months ago by • 0 • written 6.8 years ago by • 0
0
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4
replies
1.1k
views
Fix regions for bumphunter
bumphunter DMR methylation minfi
4.9 years ago i.s.brorson • 0
0
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2
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1.0k
views
Bumphunter output "regions" of 1 probe (L =1)
DMR bumphunter EPIC chip
4.9 years ago i.s.brorson • 0
0
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1
reply
1.1k
views
Error:package or namespace load failed for 'bumphunter': object "path" is not exported by namespace:Rsamtools
minfi bumphunter Rsamtools
5.5 years ago Boran Gao • 0
2
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4
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1.7k
views
bumphunter stalls on "Smoothing coefficients"
bumphunter ChAMP
updated 5.6 years ago by ▴ 290 • written 5.6 years ago by ▴ 10
6
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5
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1.6k
views
dmrseq installation failed
installation problem dmrseq bumphunter
updated 6.1 years ago by 4.1k • written 6.1 years ago by ▴ 10
0
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3
replies
2.4k
views
Dependency installation error due to no longer available CRAN packages ('rngtools', 'pkgmaker')
installation minfi bumphunter
updated 6.6 years ago by ▴ 740 • written 6.6 years ago by • 0
2
votes
6
replies
2.2k
views
Bumphunting for longitudinal data
bumphunter minfi lmer dmrcate dmr analysis
updated 6.6 years ago by ▴ 200 • written 6.6 years ago by • 0
0
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2
replies
1.7k
views
Bumphunter error: subscript out of bounds
bumphunter DMR doparallel multicore
updated 17 months ago by • 0 • written 6.6 years ago by • 0
1
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5
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2.7k
views
Meaning of the value column in bumphunter output (minfi package)
minfi bumphunter
updated 6.8 years ago by • 0 • written 7.6 years ago by • 0
1
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0
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1.6k
views
Issue with bumphunter and TxDb.Hsapiens.UCSC.hg38.knownGene that could be due to S4Vectors or an installation problem
s4vectors bumphunter txdb.hsapiens.ucsc.hg38.knowngene
7.2 years ago Leonardo Collado Torres ★ 1.1k
2
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8
replies
4.5k
views
"minfi" loading problem because of couldn't "bumphunter" load
bumphunter minfi loading error rtracklayer
updated 7.6 years ago by • 0 • written 7.6 years ago by ▴ 10
1
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3
replies
1.7k
views
coef in dmrcate
dmrcate bumphunter methylation epic
updated 7.7 years ago by 67k • written 7.7 years ago by ▴ 10
0
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3
replies
2.1k
views
Controlling for confounding variables in bumphunter
minfi bumphunter confounders
updated 7.7 years ago by 67k • written 7.7 years ago by • 0
0
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1
reply
1.8k
views
"Error in NSBS - subscript contains NAs or out-of-bounds indices" for bumphunter `matchGenes`
bumphunter
7.8 years ago jon.barenboim • 0
0
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0
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1.6k
views
bumphunter P values and significance testing
minfi bumphunter
7.8 years ago cardenasca ▴ 40
4
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4
replies
3.4k
views
bumphunter output clarification: p values achieved with b=1000: further correction needed?
methylation dmr analysis bumphunter
updated 8.0 years ago by 67k • written 8.0 years ago by • 0
1
vote
4
replies
4.8k
views
bumphunter output clarification
bumphunter DMR DMR analysis minfi bioconductor
updated 8.0 years ago by ▴ 60 • written 8.0 years ago by • 0
0
votes
4
replies
2.4k
views
Using Bumphunter and SVA together in Minfi: bumphunterEngine nullMethod warning and FWER calculations
minfi sva bumphunter
8.1 years ago • updated 8.0 years ago brhead ▴ 40
6
votes
2
replies
4.8k
views
Plotting Differentially Methylated Regions
minfi bumphunter 450k region
updated 8.0 years ago by ▴ 80 • written 8.8 years ago by ▴ 40
0
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1
reply
1.3k
views
Bumphunter Algorithm Returns Regions with very few CpGs
bumphunter minfi
written 8.2 years ago by • 0
2
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6
replies
1.7k
views
bumphunter of multi covariates
bumphunter
8.3 years ago Asma rabe ▴ 290
0
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3
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1.3k
views
minfi devel error
bumphunter
updated 8.4 years ago by 25k • written 8.4 years ago by ▴ 290
0
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2
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1.3k
views
Runing into error while trying GRanges from R
rnaseq bumphunter genomicranges
8.5 years ago alva.james • 0
0
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1
reply
1.3k
views
error when using bumphunter package with illumina 450k data
minfi bumphunter DNA methylation illumina450k
updated 8.5 years ago by 67k • written 8.5 years ago by • 0
2
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9
replies
3.1k
views
bumphunter beta values
methylation minfi bumphunter
updated 8.7 years ago by 67k • written 8.7 years ago by ▴ 50
0
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0
replies
1.2k
views
How to retrieve the (smoothed) baseline values from the bumphunting output object?
bumphunter
8.9 years ago fabian.schroeder • 0
1
vote
2
replies
3.6k
views
minfi, bumphunter + complex experimental design, and 3 other 450K queries
GO convert minfi bumphunter GO convert minfi bumphunter
updated 8.9 years ago by ▴ 30 • written 10.6 years ago by ★ 4.1k
0
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3
replies
2.2k
views
Paired samples and interactions models with bumphunter?
minfi bumphunter design and contrast matrix paired samples limma
8.9 years ago david.watson ▴ 30
1
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0
replies
1.3k
views
News: Bug found and fixed in bumphunter's bootstrap method
bumphunter News
9.2 years ago rafa ▴ 60
3
votes
6
replies
2.4k
views
Complex Model Design with Bumphunter (Minfi)
minfi bumphunter model.matrix linear model
updated 21 months ago by • 0 • written 9.4 years ago by ▴ 370
0
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0
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943
views
Bumphunter Output Details
bumphunter
9.7 years ago andrew.j.skelton73 ▴ 370
4
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10
replies
3.2k
views
Using bumphunter with non-human genomes
bumphunter
updated 9.9 years ago by ★ 1.1k • written 10.1 years ago by ▴ 40
3
votes
5
replies
2.4k
views
bumphunter::annotateNearest with non-human genome
bumphunter
updated 9.9 years ago by ★ 1.1k • written 10.1 years ago by ▴ 40
2
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1
reply
2.4k
views
News: Changes to matchGenes in bumphunter
annotation bumphunter News
updated 10.0 years ago by 43k • written 10.0 years ago by ▴ 60
0
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3
replies
2.4k
views
smoothing function in bumphunter in minfi
minfi bumphunter minfi bumphunter
10.5 years ago Kasper Daniel Hansen ★ 6.5k
0
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1
reply
1.8k
views
loessByCluster returning error in smooth function in bumphunter
bumphunter bumphunter
10.6 years ago Jiayi Sun ▴ 40
0
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0
replies
1.6k
views
minfi release 1.8
SNP Annotation GO probe SNPlocs PROcess minfi bumphunter ChAMP SNP Annotation GO probe
10.6 years ago swarmqq@gmail.com ▴ 10
2
votes
1
reply
1.9k
views
smoothing function in bumphunter in minfi
minfi bumphunter minfi bumphunter
updated 10.6 years ago by ★ 6.5k • written 10.6 years ago by ★ 13k
0
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5
replies
3.8k
views
doParallel with Bumphunter gives Error in mcfork()
minfi bumphunter minfi bumphunter
updated 10.7 years ago by ★ 4.2k • written 10.7 years ago by ★ 13k
0
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0
replies
1.9k
views
DMR identification: minfi speed, memory problems
Annotation convert minfi methyAnalysis bumphunter Annotation convert minfi methyAnalysis
10.8 years ago Allegra Petti ▴ 120
0
votes
6
replies
3.3k
views
DMR identification: minfi speed, memory problems
Annotation convert minfi methyAnalysis bumphunter Annotation convert minfi methyAnalysis
updated 10.8 years ago by 67k • written 10.8 years ago by ★ 13k
0
votes
12
replies
3.3k
views
bumphunter DMRs difficulties
PROcess minfi bumphunter PROcess minfi bumphunter
updated 10.8 years ago by ★ 6.5k • written 10.8 years ago by ▴ 160
0
votes
3
replies
2.2k
views
minfi release 1.8
SNP Annotation GO probe SNPlocs PROcess minfi bumphunter ChAMP SNP Annotation GO probe
updated 10.9 years ago by ▴ 20 • written 10.9 years ago by ★ 4.2k
0
votes
0
replies
1.4k
views
minfi release 1.8
SNP Annotation minfi bumphunter SNP Annotation minfi bumphunter
10.9 years ago C T ▴ 20
50 results • Page 1 of 1
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Answer: Cross-validation with multiple control subgroups in limma by Gordon Smyth 52k
limma doesn't do cross-validation or resampling. Like most classical linear modeling procedures in statistics, limma uses a statistical mod…
Comment: Issues with seqlevelsStyle when making custom txdb objects for genomes/annotatio by Robert Castelo ★ 3.4k
Hi Hervé, thank you very much for your input into how to properly build and manage TxDb objects. gDNAx has two main inputs, one or more BAM…
Comment: Biostrings: Error writing long reads (>200 kbps) with writeQualityScaledXStringS by Aidan ▴ 60
Quick update: this is fixed in a branch awaiting PR to Biostrings (https://github.com/Bioconductor/Biostrings/pull/122). Should be in `deve…
Answer: Can DESeq2's design compensate for sequencing experimental design shortcomings? by Michael Love 43k
For statistical analysis plans, I recommend working with a local statistician or someone familiar with linear models in R. I have to reserv…
Comment: how should I apply "cpg.annotate" to TCGA methylation data in hg38 for HM450K? by xiaofeiwang198266 • 0
Thanks for your reply!
Votes
C: edgeR and lack of counts ID on CPM matrix
A: DESeq2 Following RSEM
A: importing RSEM data into DESeq2
A: Expected counts from RSEM in DESeq2
A: Using RSEM reads for DESeq2
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