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minfi
•
reset
4
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5
replies
5.9k
views
minfi support of illumina Infinium methylationEPIC v2.0
methylationEPICv2.0
minfi
updated 6 months ago by
jay
• 0 • written 13 months ago by
luca.s
▴ 50
3
votes
2
replies
460
views
What is the meaning of "CpG interrogation" and "single nucleotide extension(SBE)"?
SBE
CpG
minfi
CpGinterrogation
4 months ago
kyj2226
• 0
2
votes
6
replies
1.4k
views
How to get DMR for Infinium methylation EPIC v2
ChAMP
DMRcate
minfi
updated 4 weeks ago by
Tim Peters
▴ 180 • written 5 months ago by
rae.alshammari
▴ 10
1
vote
4
replies
201
views
minfi::read.metharray.exp
minfiData
minfi
updated 10 days ago by
Basti
▴ 780 • written 12 days ago by
clacarion
• 0
0
votes
0
replies
256
views
Normalization in methylation analysis
Methylation
minfi
preprocessQuantile
MethylationArrayData
preprocessFunnorm
4 months ago
kyj2226
• 0
0
votes
2
replies
570
views
ageData (minfi pipeline)
ageData
missMethyl
differentialvariability
minfi
updated 5 weeks ago by
CHEN
• 0 • written 11 months ago by
Saanchi
• 0
0
votes
1
reply
395
views
Two EPIC Methylation Array Analysis Questions
minfiDataEPIC
minfi
updated 8 months ago by
James W. MacDonald
65k • written 8 months ago by
phelankj
• 0
0
votes
14
replies
1.9k
views
Error while preprocessing raw data from methylation array using minfi package
minfi
updated 3 months ago by
nguyen
• 0 • written 8 months ago by
Deepa
• 0
0
votes
3
replies
934
views
Batch correction using control probes in EPIC array data
RnBeads
minfiData
minfi
EPICarray
updated 11 months ago by
Basti
▴ 780 • written 11 months ago by
Jitendra
▴ 10
0
votes
3
replies
560
views
minfi bumphunter - probe IDs
minfi
bumphunter
updated 7 months ago by
Basti
▴ 780 • written 7 months ago by
dorota.komar
• 0
0
votes
2
replies
1.4k
views
Error processing Infinium 450K Methylation data using Minfi
minfi
software error
methylation
illumina450k
updated 11 months ago by
kuzn.di
• 0 • written 8.4 years ago by
pm2015
• 0
0
votes
1
reply
318
views
Error in reading my csv file in minfi
minfiDataEPIC
minfi
updated 5 months ago by
Basti
▴ 780 • written 5 months ago by
Ana
• 0
0
votes
4
replies
241
views
Minfi - estimatecellscount
min
minfi
updated 5 days ago by
James W. MacDonald
65k • written 5 weeks ago by
clacarion
• 0
0
votes
9
replies
3.1k
views
clarification about bumphunter value output
minfi
bumphunter
updated 11 months ago by
Jennifer Dehner
• 0 • written 6.2 years ago by
src3
• 0
0
votes
0
replies
192
views
Can MethylationEPIC v1 and v2 data be used together for analysis with minfi?
minfi
minfiDataEPIC
8 weeks ago
Felix
• 0
0
votes
7
replies
456
views
error in reading idat files and creating rgset
minfi
MethylationArray
updated 11 weeks ago by
James W. MacDonald
65k • written 11 weeks ago by
sharangiiv
• 0
0
votes
5
replies
921
views
minfi, limma, adjusting for cell counts - integrating the resoults of estimateCellCounts into the linear regression model
minfi
limma
6 months ago
dorota.komar
• 0
0
votes
2
replies
661
views
minfi differential methylation analysis errors
minfi
6 months ago
matthew.sinton
• 0
0
votes
1
reply
180
views
Matrix multiplication error to estimate telomere length
methylclockData
minfi
methylclock
minfidata
updated 9 weeks ago by
James W. MacDonald
65k • written 9 weeks ago by
sharangiiv
• 0
0
votes
2
replies
526
views
EPIC array hg38 annotation?
minfi
DMRcate
12 weeks ago • updated 11 weeks ago
mycetes
• 0
0
votes
11
replies
3.7k
views
bug in cpg.annotate() and DMR.plot: bad defaults for what and arraytype arguments
DMRcate
minfi
updated 3 months ago by
Tim Peters
▴ 180 • written 7.1 years ago by
Jenny Drnevich
★ 2.0k
21 results • Page
1 of 1
Recent ...
Replies
Answer: Once again a "Model matrix not full rank"
by
swbarnes2
★ 1.3k
Replicate numbers, like the 1 in control_1 are fine in sample names, but never add them to anything else in colData. From the computer's p…
Answer: limma Intercept vs No-intercept models completely changing DMR results?
by
Gordon Smyth
50k
I'll add a little bit of general advice to James' answer. You seem to have the misunderstanding that you can change the design matrix but …
Answer: package goseq seems to be not available on the latest version of R
by
Gordon Smyth
50k
It is true that goseq isn't available for Bioc 3.19. That is because goseq depends on txbmaker, which is itself not yet available for Bioc…
Answer: limma Intercept vs No-intercept models completely changing DMR results?
by
James W. MacDonald
65k
This part: ``` design_intercept <- model.matrix(~Alt+Sex+Age+PC1, data=targets_Sherpa) colnames(design_intercept) <- c("AltSHP_LA","Al…
Comment: CombineArrays for EPIC and EPIC V2
by
Kim
• 0
Thank you Tim, this is a great help in getting me started!
Votes
Answer: limma Intercept vs No-intercept models completely changing DMR results?
Answer: CombineArrays for EPIC and EPIC V2
Answer: Too many significant genes when integrating gtex and tcga
Comment: Too many significant genes when integrating gtex and tcga
A: Print Differentially Expressed Exons From Dexseq Results
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