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Showing :
450K
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6
votes
3
replies
9.7k
views
Minfi issue: return code from pthread_create() is 22
minfi
450k
updated 13 months ago by
Sin
• 0 • written 4.8 years ago by
jshouse
▴ 10
0
votes
6
replies
5.9k
views
ComBat with multiple batches
sva
combat
450k
8.3 years ago
ben.run974
• 0
4
votes
10
replies
4.4k
views
Illumina MethylationEPIC vs. 450K
methylumi
minfi
illuminahumanmethylation450k.db
450k
methyanalysis
updated 8.2 years ago by
Peter Hickey
▴ 740 • written 8.2 years ago by
Ahdee
▴ 50
6
votes
2
replies
4.2k
views
Plotting Differentially Methylated Regions
minfi
bumphunter
450k
region
updated 7.4 years ago by
Dimitris Polychronopoulos
▴ 80 • written 8.1 years ago by
cardenasca
▴ 40
0
votes
1
reply
4.1k
views
methyAnalysis M values and Beta Values
methyAnalysis
methyanalysis
450k
updated 9.1 years ago by
Pan Du
▴ 80 • written 9.1 years ago by
andrew.j.skelton73
▴ 370
1
vote
7
replies
3.3k
views
Loading beta values into minfi
minfi
450k
updated 8.5 years ago by
Kasper Daniel Hansen
★ 6.5k • written 8.5 years ago by
CC
▴ 10
3
votes
3
replies
3.2k
views
Adjustment of covariates in 450k data using Limma
limma
covariates
450k
8.1 years ago • updated 8.0 years ago
AST
▴ 60
6
votes
3
replies
3.1k
views
Limma on Methylation Data - Fold Change Question
limma
450k
updated 8.8 years ago by
Aaron Lun
★ 28k • written 8.8 years ago by
andrew.j.skelton73
▴ 370
4
votes
4
replies
2.9k
views
How to remove unwanted probes before normalization in 450k data
minfi
450k
champ
rnbeads
updated 8.1 years ago by
James W. MacDonald
65k • written 8.1 years ago by
AST
▴ 60
0
votes
4
replies
2.4k
views
preprocessFunnorm in minfi
minfi
450k
illuminahumanmethylation450k.db
normalization
updated 8.3 years ago by
James W. MacDonald
65k • written 8.3 years ago by
b.tawk
• 0
1
vote
2
replies
2.3k
views
Bias correction for enrichment analysis of 450k methylation data => feed bias adjusted genes into IPA
goseq
450k
enrichment
updated 9.2 years ago by
belinda.phipson
▴ 40 • written 9.2 years ago by
Ed Schwalbe
▴ 10
0
votes
2
replies
2.0k
views
Error using Bumphunter and Block finder using CHAMP
champ
methylation
450k
7.4 years ago
hrishi27n
▴ 20
0
votes
1
reply
1.9k
views
News:
Bug in ChAMP package champ.SVD() function
champ
methylation
450k
SVD
EPIC
News
7.6 years ago
Yuan Tian
▴ 90
1
vote
6
replies
1.9k
views
Reading 450k data in minfi
450K
minfi
updated 5.1 years ago by
laurenz.holcik
• 0 • written 5.2 years ago by
lalchungnungabt17
• 0
1
vote
2
replies
1.9k
views
QC/normalization standards for cancer studies with 450k array data
minfi
watermelon
cancer
450k
normalization
updated 8.8 years ago by
Kasper Daniel Hansen
★ 6.5k • written 8.8 years ago by
metamaden
▴ 10
0
votes
1
reply
1.8k
views
How to analyse 450k and EPIC methylation data together?
minfi
450k
EPIC
analysis
updated 4.6 years ago by
James W. MacDonald
65k • written 4.6 years ago by
maduran
• 0
0
votes
2
replies
1.7k
views
Loading RData files into ChAMP
microarray
champ
450k
updated 8.5 years ago by
champ450k
• 0 • written 8.5 years ago by
CC
▴ 10
0
votes
4
replies
1.7k
views
Use of confounders in downstream analysis
limma
GSA
confounding
within-pair analysis
450k
9.0 years ago
Aileen Bahl
▴ 10
3
votes
6
replies
1.6k
views
Minfi can't combineArrays
RGset
combinearrays
450k
minfi
updated 2.7 years ago by
James W. MacDonald
65k • written 2.7 years ago by
Sophie Marion de Proce
• 0
2
votes
1
reply
1.6k
views
Minfi: estimateCellCounts rgSet
minfi
450k
flowsorted.blood.450k
updated 7.4 years ago by
Habil Zare
▴ 200 • written 8.0 years ago by
cardenasca
▴ 40
0
votes
0
replies
1.4k
views
minfi v1.14 through champ: read.450k error with file path name
minfi
champ
illumina
450k
8.7 years ago
jeroen
• 0
0
votes
0
replies
1.4k
views
How can I do paired test on my Illumina 450k idat files with ChAMP package?
Illumina
450k
ChAMP
paired test
8.2 years ago
walter_teng
• 0
0
votes
0
replies
1.4k
views
News:
ChAMP2 is online
epigenetics
EPIC
450K
ChAMP
News
7.5 years ago
Yuan Tian
▴ 90
0
votes
0
replies
1.4k
views
minfi estimateCellCounts normalized beta values adjusted for cell type
minfi
450k
6.9 years ago
igor
▴ 40
0
votes
3
replies
1.3k
views
QC and normalization of 450K data from CSVs instead of IDATs
450K
CSV
normalization
minfi
ChAMP
updated 5.9 years ago by
Yuan Tian
▴ 270 • written 5.9 years ago by
Simone
▴ 180
0
votes
0
replies
1.3k
views
Repetitive motifs on Illumina 450k derived sequences
illumina
450k
motifs
meme
8.3 years ago
Gustavo Fernández Bayón
▴ 440
3
votes
1
reply
1.2k
views
two 450K methylation array manifests. where is the difference?
methylation
450k
8.2 years ago
Pablo marin-garcia
▴ 90
0
votes
0
replies
1.2k
views
Error when using Champ.SVD() function
champ
champs.svd()
450K
illimina 450k methylation
champ 2.8.9
6.6 years ago
david.ch
• 0
0
votes
3
replies
1.2k
views
Limma for cell components effect on response
450k
EPIC
minfi
limma
cell components
updated 4.8 years ago by
Aaron Lun
★ 28k • written 4.8 years ago by
antgomo
• 0
0
votes
0
replies
1.1k
views
Error in assay colnames when using readGEORawFile function in "minfi" package
minfi
methylation
450k
7.4 years ago
moonkinwen
• 0
0
votes
0
replies
954
views
how to analyze "Beta-score" and get CNVdata using Comunee
conumee
CNV
450K
6.2 years ago
bird.of.clockwise
• 0
0
votes
0
replies
684
views
Error when trying to read in idat files in methylumi
methylumi
450k
methylation
methylome
4.3 years ago
A
▴ 40
0
votes
0
replies
396
views
cpgCollapse error
450K
blockfinder
cpgCollapse
minfi
13 months ago
edward.esiribloom
• 0
33 results • Page
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Recent ...
Replies
Comment: Which input file is used for DGEList in EgdeR?
by
i.atanasoai
• 0
Understood, Thank you very much for the reply, very kind.
Comment: Which input file is used for DGEList in EgdeR?
by
Michael Love
41k
"gene_counts_length_scaled.tsv file generated by the nf-core be exactly that?" No that is the counts scaled by the length. Counts + offset…
Comment: DESeq2 a lot of genes showing up as differentially expressed that only have 1 sa
by
Michael Love
41k
These genes are fine. They are just the ones where, by chance, the sample variance is below the sample mean. It happens. DESeq2 brings thes…
Comment: DEG with low counts
by
Michael Love
41k
These counts are too low, only a few samples above a count of 10. So for typical RNA-seq data that is underpowered to call differences. It…
Comment: DESeq filtering specific to contrasts
by
Michael Love
41k
If the counts are too low it in one group then you can't make the comparison either way (whether they are filtered out or just under-powere…
Votes
A: Docker container with bioconductor and devtools
Answer: OrgDb for maize
Comment: significant difference of p-values with dream() after updating VariancePartition
How to tell and visualize up/down regulation of pathways from clusterprofiler gsea output
Comment: DEXSeq DEXSeqDataSet count matrix duplication
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