Showing : Methylumi • reset
4
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10
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4.4k
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Illumina MethylationEPIC vs. 450K
methylumi minfi illuminahumanmethylation450k.db 450k methyanalysis
updated 8.2 years ago by ▴ 740 • written 8.2 years ago by ▴ 50
2
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4
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2.6k
views
Problem in installing Bioconductor packages due to "IRanges"
lumi methylumi methyAnalysis
6.3 years ago topijush ▴ 10
1
vote
2
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1.5k
views
lumi package fails to load because of a missing dependency (bumphunter)
lumi methylumi
updated 5.5 years ago by ▴ 50 • written 5.5 years ago by ▴ 30
1
vote
1
reply
721
views
Valid to normalise MethylumiSet using minfi?
normalization minfi methylumi
updated 5.1 years ago by 65k • written 5.1 years ago by • 0
1
vote
10
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3.0k
views
minfi, lumi, methylumi, DMRcate installation error
minfi lumi methylumi dmrcate illuminahumanmethylation450kanno.ilmn12.hg19
updated 7.1 years ago by ▴ 170 • written 7.1 years ago by ▴ 10
1
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1
reply
1.2k
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Filtering by bead count
methylumi
updated 8.2 years ago by ★ 6.5k • written 8.2 years ago by ▴ 400
1
vote
1
reply
609
views
Problems installing methylumi package
methylumi
updated 17 months ago by ★ 6.5k • written 17 months ago by • 0
1
vote
1
reply
945
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Subsetting samples and columns of a MethyLumiSet subsets QC probes
methylumi
updated 6.5 years ago by 21k • written 6.5 years ago by ▴ 160
0
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0
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969
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Results of QC of Demodata included in the package, HumMeth27QCReport
Normalization lumi methylumi Normalization lumi methylumi
13.4 years ago Francesco Mancuso ▴ 40
0
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2
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1.1k
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memory problem
Normalization lumi methylumi Normalization lumi methylumi
updated 12.9 years ago by ▴ 620 • written 12.9 years ago by 21k
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0
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1.8k
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reading with lumi
Preprocessing PROcess lumi methylumi Preprocessing PROcess lumi methylumi
12.2 years ago Tim Triche ★ 4.2k
0
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3
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1.5k
views
'parallel' vs 'multicore'
methylumi methylumi
updated 12.6 years ago by 25k • written 12.6 years ago by ★ 4.2k
0
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0
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1.1k
views
Error in doing QC for 450K IlluminaHumanMeth data using methylumi
methylumi methylumi
12.4 years ago Shruti Rastogi ▴ 10
0
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1
reply
1.2k
views
minfi
methylumi minfi methylumi minfi
updated 12.3 years ago by ★ 6.8k • written 12.4 years ago by ▴ 400
0
votes
2
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2.9k
views
convert between MethylLumiSet (methylumi) and RGChannelSet (minfi)
methylumi minfi methylumi minfi
updated 12.2 years ago by ★ 4.2k • written 12.2 years ago by ▴ 170
0
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0
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999
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methylumi on Infiniium27k idat files
methylumi methylumi
11.9 years ago Briggs, Chris ▴ 20
0
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1
reply
1.2k
views
qcplot() error in methylumi?
methylumi methylumi
updated 12.1 years ago by ★ 4.2k • written 12.1 years ago by ▴ 10
0
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0
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968
views
Bioconductor Digest, Vol 110, Issue 11
Normalization Cancer lumi methylumi Normalization Cancer lumi methylumi
12.0 years ago Pan Du ▴ 440
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0
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1.0k
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Large datasets in methylumi
methylumi methylumi
11.4 years ago Guest User ★ 13k
0
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0
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939
views
[methylumi] concerning methylumi.bgcorr function and out-of-band intensities
methylumi methylumi
11.3 years ago Dylan Aïssi ▴ 30
0
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1
reply
1.3k
views
Question on Analyzing Illumina 450k methylation data
methylumi methylumi
11.2 years ago Srinivas Srikanth ▴ 70
0
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0
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1.9k
views
how to use MethyLumiM object in BMIQ(wateRmelon)
lumi methylumi lumi methylumi
11.0 years ago Guest User ★ 13k
0
votes
0
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852
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[methylumi] concerning methylumi.bgcorr function and out-of-band intensities
methylumi methylumi
11.0 years ago Hannah Elliott ▴ 10
0
votes
1
reply
1.4k
views
problem with 'FDb.InfiniumMethylation.hg19'
BSgenome BSgenome lumi methylumi BSgenome BSgenome lumi methylumi
updated 10.8 years ago by ▴ 120 • written 10.8 years ago by 65k
0
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2
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2.3k
views
Disparity between MethylLumiSet (methylumi) and RGChannelSet (minfi) - treatment of missing values
probe methylumi probe methylumi
updated 10.8 years ago by ★ 6.5k • written 10.8 years ago by ▴ 20
0
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0
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972
views
MethyLumiM to MethyLumiSet?
convert lumi methylumi convert lumi methylumi
10.5 years ago Allegra Petti ▴ 120
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1
reply
1.5k
views
MethylSet to MethyLumiSet
minfi methylumi watermelon
7.2 years ago Tom ▴ 10
0
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7
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2.2k
views
methyAnalysis error
GO convert methylumi genoset GO convert methylumi genoset
10.5 years ago Juan Fernández Tajes ▴ 190
0
votes
6
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3.9k
views
Removing sex-chromosome probes from methyLumiSet
methylumi eSet illuminahumanmethylation450k.db featureFilter
updated 8.8 years ago by 65k • written 8.8 years ago by • 0
0
votes
5
replies
2.0k
views
Is it possible to convert Methylumi object into RGChannelSet
microarray minfi methylumi illumina450k
7.4 years ago • updated 6.6 years ago poojitha.stemcell ▴ 10
0
votes
2
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1.4k
views
Error while using BMIQ normalisation on a methylumiSet
limma watermelon methylumi bmiq
updated 7.4 years ago by ▴ 10 • written 7.4 years ago by ▴ 10
0
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0
replies
1.2k
views
how to use Methylumi background correction (noob) in CHAMP
Methylumi NOOB CHAMP Background corection illimina 450k methylation
7.1 years ago rahel14350 ▴ 10
0
votes
0
replies
1.3k
views
Can't get the lumi and methylumi packages to work.
lumi methylumi
6.9 years ago gitteba • 0
0
votes
0
replies
688
views
Error when trying to read in idat files in methylumi
methylumi 450k methylation methylome
4.3 years ago A ▴ 40
0
votes
2
replies
1.0k
views
Convert MethyLumiSet into RGChannelSet (Illumina EPIC methylation data)
methylumi minfi microarray epic
4.0 years ago • updated 3.5 years ago Nala • 0
0
votes
10
replies
2.2k
views
MethyLumiM to MethyLumiSet?
convert lumi methylumi minfi wateRmelon convert lumi methylumi minfi wateRmelon
updated 10.5 years ago by ★ 4.2k • written 10.5 years ago by ▴ 190
0
votes
2
replies
1.2k
views
methylumi
Microarray methylumi Microarray methylumi
updated 14.3 years ago by 21k • written 14.3 years ago by ▴ 70
0
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0
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1.1k
views
methylumiSet - normalization
methylumi methylumi
13.8 years ago Noemi Andor ▴ 100
0
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0
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827
views
methylumi: Quality Control
limma methylumi limma methylumi
13.8 years ago Jinyan Huang ▴ 50
0
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1
reply
1.1k
views
Illumina GoldenGate methylation array, methylumi
limma methylumi limma methylumi
updated 13.7 years ago by ▴ 350 • written 13.7 years ago by ▴ 10
0
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0
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974
views
about normalizeMethyLumiSet
methylumi methylumi
13.7 years ago gregory voisin ▴ 430
0
votes
2
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1.2k
views
Cy5: methylated or unmethylated?
methylumi methylumi
updated 13.6 years ago by 21k • written 13.6 years ago by ▴ 720
0
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3
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1.6k
views
Data from GEO in Methylumi
methylumi methylumi
updated 13.6 years ago by 21k • written 13.6 years ago by ▴ 90
43 results • Page 1 of 1
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Comment: How to retrieve gene ontology GO class from gene list? by bandconductor • 0
Thanks, this is potentially a much faster way than parsing BiomRt. However, it is only returning one GO term right now (biomaRt returns a f…
Comment: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2 by James W. MacDonald 65k
Both `RUVseq` and `sva` are meant to be used to remove technical variability. The problem is the identification of variability that is tech…
Comment: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2 by Alexandre • 0
Hello James, Thank you very much for your answer and taking the time to read my post. I understand your remark, but isn't the approach o…
Comment: PCA plot suggestions by JKim • 0
cross post: https://www.biostars.org/p/9593486/
Answer: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2 by James W. MacDonald 65k
You cannot correct for technical variability due to batch if samples are nested in batch. The technical and biological differences are comp…
Votes
Answer: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
Answer: Use of negative binomial model for exponential decay rate estimation using DESeq
C: null model and DEXSeqDataSet object in DEXSEQ
A: Are published RNA seq data analyses often wrong in calculating p-values and FDR?
A: How to explain how DESeq2 works to someone with zero bioinformatics background?
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