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watermelon
•
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541
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A survey of computational setups for Illumina Infinium DNA methylation EPIC array pipeline
DNAMethylation
wateRmelon
Computation
minfi
21 months ago
calen.p.ryan
• 0
0
votes
7
replies
1.0k
views
Getting wrong rownames of MSet object when using pfilter from watermelon
wateRmelon
Illumina EPIC
pfilter
updated 4.5 years ago by
lschal
• 0 • written 4.5 years ago by
anne-kristin.stavrum
• 0
1
vote
3
replies
1.5k
views
Combining pfilter (wateRmelon) and preprocessNoob (minfi)
wateRmelon
minfi
methylation
pfilter
preprocessNoob
updated 4.7 years ago by
tgorri
▴ 10 • written 4.7 years ago by
sara.blocquiaux
• 0
0
votes
0
replies
1.1k
views
Error in ENmix::bmiq.mc(): BMIQ estimates encountered error, try to run it again
methylation
ENmix
BMIQ
wateRmelon
5.2 years ago
moldach
▴ 20
0
votes
1
reply
1.5k
views
MethylSet to MethyLumiSet
minfi
methylumi
watermelon
7.3 years ago • updated 7.2 years ago
Tom
▴ 10
0
votes
5
replies
2.2k
views
Different errors when attempting to normalize using wateRmelon (v1.1.18)
wateRmelon
methylation
EPIC
normalization
7.3 years ago
Wade Davis
▴ 60
0
votes
2
replies
1.4k
views
Error while using BMIQ normalisation on a methylumiSet
limma
watermelon
methylumi
bmiq
updated 7.4 years ago by
tgorri
▴ 10 • written 7.4 years ago by
poojitha.stemcell
▴ 10
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
3
replies
2.0k
views
minfi getProbeInfo error ( was WateRmelon betaqn error)
watermelon
betaqn
pfilter
getProbeInfo
minfi
9.2 years ago
gctromp
▴ 10
0
votes
10
replies
2.2k
views
MethyLumiM to MethyLumiSet?
convert
lumi
methylumi
minfi
wateRmelon
convert
lumi
methylumi
minfi
wateRmelon
updated 10.5 years ago by
Tim Triche
★ 4.2k • written 10.5 years ago by
Martin Rijlaarsdam
▴ 190
10 results • Page
1 of 1
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Answer: Method to find pathways different between 2 groups
by
Gordon Smyth
50k
> When I search camera limma on pubmed, I found 2 papers I am unclear what point you are trying to make. limma's camera method has been fo…
Comment: package goseq seems to be not available on the latest version of R
by
Gordon Smyth
50k
limma most certainly is available. It installs in R 4.4.0 and Bioc 3.19 for all platforms without any issues. It has not had any period of …
Comment: package goseq seems to be not available on the latest version of R
by
Patrycja
▴ 20
limma package also isn't available.Is there any information when these packages will be available?
Comment: How to use bootRanges to bootstrap small RNA loci (nullranges package)
by
Michael Love
41k
Check the number of bootstrapped data per chromosome compared to the original, and then you can also look at its distribution. For this it'…
Comment: DNAString: Standard checksum function?
by
Henrik Bengtsson
★ 2.4k
For completeness: SEGUID v2 (https://www.seguid.org/), implemented in CRAN package **[seguid](https://cran.r-project.org/package=seguid)*…
Votes
Answer: Why does GSEA on edgeR results for randomized samples give highly significant p-
Handling multiple differential expression comparisons
Answer: fgsea significant result
Answer: fgsea significant result
package goseq seems to be not available on the latest version of R
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ATpoint
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Ben
▴ 50
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Sam
▴ 10
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Gordon Smyth
50k
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Zainab
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