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illumina450k
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1.5k
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Minfi returning incorrect beta values
minfi
illumina
illumina450k
methylation
R
6.8 years ago
ezrabekele17
• 0
0
votes
1
reply
1.6k
views
Error while using ChAMP
champ
methylation
illuminahumanmethylation450k.db
illumina450k
updated 7.5 years ago by
Yuan Tian
▴ 90 • written 7.5 years ago by
hrishi27n
▴ 20
0
votes
5
replies
2.0k
views
Is it possible to convert Methylumi object into RGChannelSet
microarray
minfi
methylumi
illumina450k
7.5 years ago • updated 6.6 years ago
poojitha.stemcell
▴ 10
4
votes
8
replies
1.8k
views
Limma for paired and unpaired analysis with adjustment for categorical and continuous variables
limma
illumina450k
lmfit
updated 7.5 years ago by
Ryan C. Thompson
★ 7.9k • written 7.5 years ago by
DSP
• 0
0
votes
0
replies
922
views
Creating a GenomicRatioSet with non minfi normalized data
minfi
methylation
illumina450k
7.5 years ago
hrishi27n
▴ 20
0
votes
4
replies
2.2k
views
Error with Minfi while using read.metharray.exp() and read.metharray function
minfi
illumina450k
methylation
7.5 years ago
hrishi27n
▴ 20
0
votes
4
replies
1.8k
views
ComBat: Adjustment for 3experimental variables
ENmix
combat.mc
illumina450k
combat sva
7.8 years ago
DSP
• 0
0
votes
1
reply
1.1k
views
error when using bumphunter package with illumina 450k data
minfi
bumphunter
DNA methylation
illumina450k
updated 7.9 years ago by
James W. MacDonald
65k • written 7.9 years ago by
fleur_p90
• 0
0
votes
0
replies
1.4k
views
ChAMP ComBat step error: Error in if (min(beta.c) == 0) { : missing value where TRUE/FALSE needed
ChAMP
methylation
illumina450k
8.0 years ago
Daniel E. Weeks
▴ 30
0
votes
0
replies
807
views
illumina HM 450 data
illumina450k
methylation
8.0 years ago
niutster
• 0
0
votes
6
replies
3.2k
views
Analyzing pre/post (longitudinal) data using limma/lme4 with adjustment for continuous covariates
illumina450k
limma
lme4
lmer
updated 8.0 years ago by
Aaron Lun
★ 28k • written 8.0 years ago by
DSP
• 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
0
replies
1.2k
views
Error processing Infinium 450K Methylation data using Minfi
minfi
software error
methylation
illumina450k
8.4 years ago
pm2015
• 0
1
vote
1
reply
1.7k
views
RnBeads - doesn't produce pdfs
rnbeads
illumina450k
updated 8.5 years ago by
pavlo.lutsik
▴ 10 • written 8.5 years ago by
Brian Smith
▴ 120
14 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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