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methylationepic
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1.1k
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Beta values and M values cluster differently
methylationEPIC
minfi
microarray
epigenetics
EPIC
5.3 years ago
rmf
▴ 20
0
votes
0
replies
849
views
Best normalisation method
microarray
methylationEPIC
epigenetics
minfi
EPIC
5.3 years ago
rmf
▴ 20
3
votes
6
replies
2.1k
views
could not find function "champ.load"
ChAMP
champ 2.9.10
methylationepic
6.2 years ago
david.ch
• 0
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
2.0k
views
ChAMP Methylation analysis error code "could not find function champ.load"
champ
methylationepic
updated 6.4 years ago by
Yuan Tian
▴ 290 • written 6.4 years ago by
csappleby-mallinder1
• 0
3
votes
4
replies
3.0k
views
Error while using champ.svd() function in subset of data
ChAMP
methylationepic
epicarray
epigenomics
updated 6.7 years ago by
rcavalca
▴ 140 • written 6.7 years ago by
karthikrpad
▴ 10
0
votes
0
replies
921
views
Error when changing the database for minfi dropLociWithSnps
minfi
methylationepic
illuminahumanmethylationepicanno.ilmn10b.hg19
SNP
6.9 years ago
Ellen O
• 0
0
votes
2
replies
1.9k
views
Illumina methylationEPIC demo data in IDAT format?
methylation
illumina
EPIC
methylationepic
idat
updated 7.1 years ago by
Guido Hooiveld
★ 4.0k • written 7.1 years ago by
Ellen O
• 0
0
votes
4
replies
1.7k
views
minfi "mapToGenome" dimension error
methylation
epic microarray
minfi
methylationepic
7.3 years ago
nhejazi
• 0
0
votes
0
replies
1.0k
views
Shinymethyl 850K Array quality control signal cutoffs
shinymethyl
minfi
epic microarray
methylationepic
qualitycontrol
7.3 years ago
chelsey.ju
• 0
0
votes
3
replies
1.7k
views
MINFI missing samples in qcreports and densityplots
minfi
illumina
methylationEPIC
densityplot
7.4 years ago
annabelle.congras
▴ 10
11 results • Page
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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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swbarnes2
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Stephanie M. Gogarten
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Jonathan
▴ 10
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Frederico Moraes Ferreira
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