Showing : bumphunter • reset
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minfi - bumphunter value problem
bumphunter minfiData minfi bumphun
updated 9 months ago by 68k • written 9 months ago by • 0
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3
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1.2k
views
minfi bumphunter - probe IDs
minfi bumphunter
updated 18 months ago by ▴ 780 • written 18 months ago by • 0
0
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1
reply
955
views
specifying comparison of interest in the minfi Bumhunter function
limma bumphunter methylationArrayAnalysis minfi
updated 2.1 years ago by 68k • written 2.1 years ago by • 0
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0
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979
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Error: 'bumphunter()' only supports matrix-backed minfi objects.
bumphunter minfi genomi
2.9 years ago runye • 0
0
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0
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975
views
Does bump hunter support Infinium Mouse Methylation BeadChip Array data?
bumphunter
3.1 years ago ZHAOHUI • 0
0
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9
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3.9k
views
clarification about bumphunter value output
minfi bumphunter
updated 23 months ago by • 0 • written 7.1 years ago by • 0
0
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4
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1.3k
views
Fix regions for bumphunter
bumphunter DMR methylation minfi
5.2 years ago i.s.brorson • 0
0
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2
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1.1k
views
Bumphunter output "regions" of 1 probe (L =1)
DMR bumphunter EPIC chip
5.2 years ago i.s.brorson • 0
0
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1
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1.2k
views
Error:package or namespace load failed for 'bumphunter': object "path" is not exported by namespace:Rsamtools
minfi bumphunter Rsamtools
5.8 years ago Boran Gao • 0
2
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4
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1.9k
views
bumphunter stalls on "Smoothing coefficients"
bumphunter ChAMP
updated 5.9 years ago by ▴ 290 • written 5.9 years ago by ▴ 10
6
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5
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1.7k
views
dmrseq installation failed
installation problem dmrseq bumphunter
updated 6.5 years ago by 4.1k • written 6.5 years ago by ▴ 10
0
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3
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2.5k
views
Dependency installation error due to no longer available CRAN packages ('rngtools', 'pkgmaker')
installation minfi bumphunter
updated 7.0 years ago by ▴ 750 • written 7.0 years ago by • 0
2
votes
6
replies
2.4k
views
Bumphunting for longitudinal data
bumphunter minfi lmer dmrcate dmr analysis
updated 7.0 years ago by ▴ 230 • written 7.0 years ago by • 0
0
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2
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1.8k
views
Bumphunter error: subscript out of bounds
bumphunter DMR doparallel multicore
updated 21 months ago by • 0 • written 7.0 years ago by • 0
1
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5
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2.8k
views
Meaning of the value column in bumphunter output (minfi package)
minfi bumphunter
updated 7.1 years ago by • 0 • written 7.9 years ago by • 0
1
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0
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1.8k
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
7.6 years ago Leonardo Collado Torres ★ 1.1k
2
votes
8
replies
4.7k
views
"minfi" loading problem because of couldn't "bumphunter" load
bumphunter minfi loading error rtracklayer
updated 7.9 years ago by • 0 • written 8.0 years ago by ▴ 10
1
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3
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1.9k
views
coef in dmrcate
dmrcate bumphunter methylation epic
updated 8.0 years ago by 68k • written 8.0 years ago by ▴ 10
0
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3
replies
2.3k
views
Controlling for confounding variables in bumphunter
minfi bumphunter confounders
updated 8.1 years ago by 68k • written 8.1 years ago by • 0
0
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1
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1.9k
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"Error in NSBS - subscript contains NAs or out-of-bounds indices" for bumphunter `matchGenes`
bumphunter
8.1 years ago jon.barenboim • 0
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0
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1.6k
views
bumphunter P values and significance testing
minfi bumphunter
8.1 years ago cardenasca ▴ 40
4
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4
replies
3.6k
views
bumphunter output clarification: p values achieved with b=1000: further correction needed?
methylation dmr analysis bumphunter
updated 8.3 years ago by 68k • written 8.3 years ago by • 0
1
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4
replies
5.0k
views
bumphunter output clarification
bumphunter DMR DMR analysis minfi bioconductor
updated 8.3 years ago by ▴ 60 • written 8.3 years ago by • 0
0
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4
replies
2.6k
views
Using Bumphunter and SVA together in Minfi: bumphunterEngine nullMethod warning and FWER calculations
minfi sva bumphunter
8.4 years ago • updated 8.3 years ago brhead ▴ 40
6
votes
2
replies
5.2k
views
Plotting Differentially Methylated Regions
minfi bumphunter 450k region
updated 8.4 years ago by ▴ 80 • written 9.1 years ago by ▴ 40
0
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1
reply
1.4k
views
Bumphunter Algorithm Returns Regions with very few CpGs
bumphunter minfi
written 8.5 years ago by • 0
2
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6
replies
1.9k
views
bumphunter of multi covariates
bumphunter
8.7 years ago Asma rabe ▴ 290
0
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3
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1.3k
views
minfi devel error
bumphunter
updated 8.8 years ago by 25k • written 8.8 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
8.8 years ago alva.james • 0
0
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1
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1.4k
views
error when using bumphunter package with illumina 450k data
minfi bumphunter DNA methylation illumina450k
updated 8.9 years ago by 68k • written 8.9 years ago by • 0
2
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9
replies
3.3k
views
bumphunter beta values
methylation minfi bumphunter
updated 9.0 years ago by 68k • written 9.0 years ago by ▴ 50
0
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0
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1.3k
views
How to retrieve the (smoothed) baseline values from the bumphunting output object?
bumphunter
9.2 years ago fabian.schroeder • 0
1
vote
2
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3.7k
views
minfi, bumphunter + complex experimental design, and 3 other 450K queries
GO convert minfi bumphunter GO convert minfi bumphunter
updated 9.3 years ago by ▴ 30 • written 10.9 years ago by ★ 4.1k
0
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3
replies
2.3k
views
Paired samples and interactions models with bumphunter?
minfi bumphunter design and contrast matrix paired samples limma
9.3 years ago david.watson ▴ 30
1
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0
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1.4k
views
News: Bug found and fixed in bumphunter's bootstrap method
bumphunter News
9.5 years ago rafa ▴ 60
3
votes
6
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2.5k
views
Complex Model Design with Bumphunter (Minfi)
minfi bumphunter model.matrix linear model
updated 2.1 years ago by • 0 • written 9.8 years ago by ▴ 370
0
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0
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989
views
Bumphunter Output Details
bumphunter
10.1 years ago andrew.j.skelton73 ▴ 370
4
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10
replies
3.4k
views
Using bumphunter with non-human genomes
bumphunter
updated 10.3 years ago by ★ 1.1k • written 10.5 years ago by ▴ 40
3
votes
5
replies
2.6k
views
bumphunter::annotateNearest with non-human genome
bumphunter
updated 10.3 years ago by ★ 1.1k • written 10.4 years ago by ▴ 40
2
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1
reply
2.5k
views
News: Changes to matchGenes in bumphunter
annotation bumphunter News
updated 10.4 years ago by 43k • written 10.4 years ago by ▴ 60
0
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3
replies
2.5k
views
smoothing function in bumphunter in minfi
minfi bumphunter minfi bumphunter
10.9 years ago Kasper Daniel Hansen ★ 6.5k
0
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1
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1.9k
views
loessByCluster returning error in smooth function in bumphunter
bumphunter bumphunter
10.9 years ago Jiayi Sun ▴ 40
0
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0
replies
1.7k
views
minfi release 1.8
SNP Annotation GO probe SNPlocs PROcess minfi bumphunter ChAMP SNP Annotation GO probe
10.9 years ago swarmqq@gmail.com ▴ 10
2
votes
1
reply
2.0k
views
smoothing function in bumphunter in minfi
minfi bumphunter minfi bumphunter
updated 11.0 years ago by ★ 6.5k • written 11.0 years ago by ★ 13k
0
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5
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4.0k
views
doParallel with Bumphunter gives Error in mcfork()
minfi bumphunter minfi bumphunter
updated 11.0 years ago by ★ 4.2k • written 11.0 years ago by ★ 13k
0
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0
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1.9k
views
DMR identification: minfi speed, memory problems
Annotation convert minfi methyAnalysis bumphunter Annotation convert minfi methyAnalysis
11.2 years ago Allegra Petti ▴ 120
0
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6
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3.5k
views
DMR identification: minfi speed, memory problems
Annotation convert minfi methyAnalysis bumphunter Annotation convert minfi methyAnalysis
updated 11.2 years ago by 68k • written 11.2 years ago by ★ 13k
0
votes
12
replies
3.5k
views
bumphunter DMRs difficulties
PROcess minfi bumphunter PROcess minfi bumphunter
updated 11.2 years ago by ★ 6.5k • written 11.2 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 11.2 years ago by ▴ 20 • written 11.2 years ago by ★ 4.2k
0
votes
0
replies
1.5k
views
minfi release 1.8
SNP Annotation minfi bumphunter SNP Annotation minfi bumphunter
11.2 years ago C T ▴ 20
50 results • Page 1 of 1
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Comment: Controlling for batch and estrus cycle using DESeq2 in RNA-seq analysis by donnycrimson • 0
One potential workaround might be to adjust for these factors using a combination of design matrices perhaps including batch as a covariate…
Comment: DESeq2 Design controlling for gender by donnycrimson • 0
On a lighter note, while you are tackling such complex data, you might enjoy a quick break playing the [Slope Game](https://slopegame.lol)…
Comment: MetaDE.pvalue: Error in xj[i]: invalid subscript type 'list' by donnycrimson • 0
Have you considered streamlining how you handle data input to mitigate these issues. It might help to define the parameters more strictly …
Comment: CluserProfiler message "No gene can be mapped" by Carolina • 0
There is, the overlap that reads out is ( Genes in common: 368 of 368 ). Here is the link for [background genes][1], [term2gene][2], [term2…
Comment: Differing results with DESeq2 by JKim • 0
My two cents. I think it would be more straightforward if you use cellmeans model. Have a look at [A guide to creating design matrices for …
Votes
remove X and Y chromosome genes in RNA-seq data using DESeq2 pipeline
How to remove X & Y chromosome genes from RNAseq data
Is it advisable to remove X and Y chromosome genes in mouse bulk RNA-seq data at the level of the count matrix?
A: Unbalanced experiment with multiple samples from each patient.
A: Understanding contrasts limma
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