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DNA Methylation
•
reset
0
votes
1
reply
954
views
Estimate cell proportion from beta values using minfi estimateCellCounts?
minfi
cell proportion
estimateCellCounts
DNA Methylation
4.2 years ago
grayapply2009
• 0
1
vote
2
replies
1.9k
views
WGCNA on methylation data
normalization
DNA methylation
WGCNA
updated 5.0 years ago by
Peter Langfelder
★ 3.0k • written 5.0 years ago by
enora.fremy
• 0
1
vote
2
replies
994
views
Comparing more than 2 experimental groups with MEDIPS?
medips
medip-seq
dna methylation
dmr analysis
updated 5.5 years ago by
Lukas Chavez
▴ 570 • written 5.5 years ago by
mtefit
• 0
7
votes
7
replies
1.6k
views
Using GenomicDataCommons R package to identify cases with both DNA methylation and gene expression data
R
gdc
rna-seq
dna methylation
updated 5.6 years ago by
Sean Davis
21k • written 5.6 years ago by
RichardJActon
▴ 50
1
vote
2
replies
1.2k
views
Odd Sample after SWAN normalisation, DNA methylation analysis EPIC array
minfi
normalization
outliers
dna methylation
densityplot
5.9 years ago
peter.fransquet
• 0
0
votes
0
replies
769
views
iEVORA wrapping up error
differential variability
dna methylation
iEVORA
DVP
6.1 years ago
poojitha.stemcell
▴ 10
0
votes
0
replies
1.1k
views
differential methylation analysis with RnBeads
rnbeads
methylation
methylationepic
dna methylation
6.3 years ago
gabrielrfries
• 0
0
votes
1
reply
1.1k
views
Problem in working with BiSeq - BSraw
dna methylation
biseq
updated 6.5 years ago by
Gordon Smyth
51k • written 6.5 years ago by
ahmad.moousavi
• 0
2
votes
5
replies
1.8k
views
Error when prepare the TCGAdata
tcgabiolinks
dna methylation
updated 6.5 years ago by
Marcel Ramos
700 • written 6.5 years ago by
michaelwxf2012
• 0
1
vote
1
reply
1.5k
views
Beta Value Analysis - DNA Methylation Dataset
dna methylation
illimina 450k methylation
beta
M
significance
updated 6.7 years ago by
James W. MacDonald
66k • written 6.7 years ago by
skids121
• 0
0
votes
0
replies
1.2k
views
DNA methylation 450k data - minfi - preprocessFunnorm - CNV cases vs non-CNV controls
CNV
minfi
preprocessing
dna methylation
7.2 years ago
Thomas
• 0
1
vote
2
replies
998
views
Correlating DNA methylation and Illumina gene expression microarray data
microarray
HM450
dna methylation
cohcap
updated 7.4 years ago by
James W. MacDonald
66k • written 7.4 years ago by
poojitha.stemcell
▴ 10
0
votes
1
reply
1.1k
views
error when using bumphunter package with illumina 450k data
minfi
bumphunter
DNA methylation
illumina450k
updated 8.0 years ago by
James W. MacDonald
66k • written 8.0 years ago by
fleur_p90
• 0
13 results • Page
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Replies
Comment: gds in GEOmetadb 2023-06-26 version is empty
by
Frederico Moraes Ferreira
▴ 100
Try axel -n 20 https://gbnci.cancer.gov/geo/GEOmetadb.sqlite.gz
Comment: Most enriched pathway is not expressed when modifying universe parameter
by
James W. MacDonald
66k
The default for `enrichGO` is to subset to those with a p-value<0.05. You don't adjust that default argument, so you shouldn't have any GO …
Answer: In a 3 group DEG analysis with three batches, can I use 1 group in all three bat
by
Michael Love
42k
You can compare A and C thanks to the sharing of samples from B across 1, 2 and 3.
Comment: Most enriched pathway is not expressed when modifying universe parameter
by
adripel
• 0
In the enrichGO results we have significant and non-significant enriched terms that are displayed. So why would an enriched term (significa…
Answer: Design formula, numeric contrast, and lfcshrink in deseq2
by
Michael Love
42k
For questions about how to construct the correct contrasts correspond to particular hypotheses, I recommend consulting with a local statist…
Votes
Comment: Most enriched pathway is not expressed when modifying universe parameter
Time-course, comparison of two groups
Answer: Behaviour of featureCounts when quantifying multi-mapping reads
Answer: GESA with certain gene list returns no result with human genom, but many result
Answer: Odd behavior of Rsubread::featureCounts when setting `nonOverlap = 0`
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