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methylumi
•
reset
0
votes
7
replies
2.2k
views
methyAnalysis error
GO
convert
methylumi
genoset
GO
convert
methylumi
genoset
10.5 years ago
Juan Fernández Tajes
▴ 190
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
1
vote
10
replies
3.0k
views
minfi, lumi, methylumi, DMRcate installation error
minfi
lumi
methylumi
dmrcate
illuminahumanmethylation450kanno.ilmn12.hg19
updated 7.1 years ago by
Tim Peters
▴ 170 • written 7.1 years ago by
poojitha.stemcell
▴ 10
1
vote
2
replies
1.5k
views
lumi package fails to load because of a missing dependency (bumphunter)
lumi
methylumi
updated 5.5 years ago by
lhuang7
▴ 50 • written 5.5 years ago by
kaur.alasoo
▴ 30
0
votes
5
replies
2.0k
views
Is it possible to convert Methylumi object into RGChannelSet
microarray
minfi
methylumi
illumina450k
7.4 years ago • updated 6.6 years ago
poojitha.stemcell
▴ 10
1
vote
1
reply
1.2k
views
Filtering by bead count
methylumi
updated 8.2 years ago by
Mike Smith
★ 6.5k • written 8.2 years ago by
khadeeja ismail
▴ 400
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
0
votes
2
replies
2.9k
views
convert between MethylLumiSet (methylumi) and RGChannelSet (minfi)
methylumi
minfi
methylumi
minfi
updated 12.2 years ago by
Tim Triche
★ 4.2k • written 12.2 years ago by
Aaron Mackey
▴ 170
0
votes
3
replies
1.6k
views
Data from GEO in Methylumi
methylumi
methylumi
updated 13.6 years ago by
Sean Davis
21k • written 13.6 years ago by
S T
▴ 90
1
vote
1
reply
945
views
Subsetting samples and columns of a MethyLumiSet subsets QC probes
methylumi
updated 6.5 years ago by
Sean Davis
21k • written 6.5 years ago by
alan.ocallaghan
▴ 160
0
votes
1
reply
1.2k
views
qcplot() error in methylumi?
methylumi
methylumi
updated 12.1 years ago by
Tim Triche
★ 4.2k • written 12.1 years ago by
Oliver Lyttleton
▴ 10
1
vote
1
reply
721
views
Valid to normalise MethylumiSet using minfi?
normalization
minfi
methylumi
updated 5.1 years ago by
James W. MacDonald
65k • written 5.1 years ago by
Pem
• 0
0
votes
1
reply
1.1k
views
Illumina GoldenGate methylation array, methylumi
limma
methylumi
limma
methylumi
updated 13.7 years ago by
Davis, Wade
▴ 350 • written 13.7 years ago by
Jinyan Huang
▴ 10
0
votes
2
replies
1.1k
views
memory problem
Normalization
lumi
methylumi
Normalization
lumi
methylumi
updated 12.9 years ago by
Ina Hoeschele
▴ 620 • written 12.9 years ago by
Sean Davis
21k
0
votes
2
replies
1.2k
views
methylumi
Microarray
methylumi
Microarray
methylumi
updated 14.3 years ago by
Sean Davis
21k • written 14.3 years ago by
Paul Sanfilippo
▴ 70
0
votes
1
reply
1.3k
views
Question on Analyzing Illumina 450k methylation data
methylumi
methylumi
11.2 years ago
Srinivas Srikanth
▴ 70
0
votes
3
replies
1.5k
views
'parallel' vs 'multicore'
methylumi
methylumi
updated 12.6 years ago by
Martin Morgan
25k • written 12.6 years ago by
Tim Triche
★ 4.2k
0
votes
1
reply
1.4k
views
problem with 'FDb.InfiniumMethylation.hg19'
BSgenome
BSgenome
lumi
methylumi
BSgenome
BSgenome
lumi
methylumi
updated 10.8 years ago by
VSM
▴ 120 • written 10.8 years ago by
James W. MacDonald
65k
0
votes
2
replies
1.2k
views
Cy5: methylated or unmethylated?
methylumi
methylumi
updated 13.6 years ago by
Sean Davis
21k • written 13.6 years ago by
Shi, Tao
▴ 720
0
votes
2
replies
2.3k
views
Disparity between MethylLumiSet (methylumi) and RGChannelSet (minfi) - treatment of missing values
probe
methylumi
probe
methylumi
updated 10.8 years ago by
Kasper Daniel Hansen
★ 6.5k • written 10.8 years ago by
Pilling, Luke
▴ 20
0
votes
1
reply
1.2k
views
minfi
methylumi
minfi
methylumi
minfi
updated 12.3 years ago by
Valerie Obenchain
★ 6.8k • written 12.4 years ago by
khadeeja ismail
▴ 400
0
votes
6
replies
3.9k
views
Removing sex-chromosome probes from methyLumiSet
methylumi
eSet
illuminahumanmethylation450k.db
featureFilter
updated 8.8 years ago by
James W. MacDonald
65k • written 8.8 years ago by
martens.christopher
• 0
4
votes
10
replies
4.4k
views
Illumina MethylationEPIC vs. 450K
methylumi
minfi
illuminahumanmethylation450k.db
450k
methyanalysis
updated 8.2 years ago by
Peter Hickey
▴ 740 • written 8.2 years ago by
Ahdee
▴ 50
1
vote
1
reply
609
views
Problems installing methylumi package
methylumi
updated 17 months ago by
Mike Smith
★ 6.5k • written 17 months ago by
Alison
• 0
0
votes
0
replies
1.1k
views
methylumiSet - normalization
methylumi
methylumi
13.8 years ago
Noemi Andor
▴ 100
0
votes
0
replies
827
views
methylumi: Quality Control
limma
methylumi
limma
methylumi
13.8 years ago
Jinyan Huang
▴ 50
0
votes
0
replies
974
views
about normalizeMethyLumiSet
methylumi
methylumi
13.7 years ago
gregory voisin
▴ 430
0
votes
0
replies
969
views
Results of QC of Demodata included in the package, HumMeth27QCReport
Normalization
lumi
methylumi
Normalization
lumi
methylumi
13.4 years ago
Francesco Mancuso
▴ 40
0
votes
0
replies
1.8k
views
reading with lumi
Preprocessing
PROcess
lumi
methylumi
Preprocessing
PROcess
lumi
methylumi
12.2 years ago
Tim Triche
★ 4.2k
0
votes
0
replies
1.1k
views
Error in doing QC for 450K IlluminaHumanMeth data using methylumi
methylumi
methylumi
12.4 years ago
Shruti Rastogi
▴ 10
0
votes
0
replies
999
views
methylumi on Infiniium27k idat files
methylumi
methylumi
11.9 years ago
Briggs, Chris
▴ 20
0
votes
0
replies
968
views
Bioconductor Digest, Vol 110, Issue 11
Normalization
Cancer
lumi
methylumi
Normalization
Cancer
lumi
methylumi
12.0 years ago
Pan Du
▴ 440
0
votes
0
replies
1.0k
views
Large datasets in methylumi
methylumi
methylumi
11.4 years ago
Guest User
★ 13k
0
votes
0
replies
939
views
[methylumi] concerning methylumi.bgcorr function and out-of-band intensities
methylumi
methylumi
11.3 years ago
Dylan Aïssi
▴ 30
0
votes
0
replies
1.9k
views
how to use MethyLumiM object in BMIQ(wateRmelon)
lumi
methylumi
lumi
methylumi
11.0 years ago
Guest User
★ 13k
0
votes
0
replies
852
views
[methylumi] concerning methylumi.bgcorr function and out-of-band intensities
methylumi
methylumi
11.0 years ago
Hannah Elliott
▴ 10
0
votes
0
replies
972
views
MethyLumiM to MethyLumiSet?
convert
lumi
methylumi
convert
lumi
methylumi
10.5 years ago
Allegra Petti
▴ 120
0
votes
0
replies
1.2k
views
how to use Methylumi background correction (noob) in CHAMP
Methylumi
NOOB
CHAMP
Background corection
illimina 450k methylation
7.1 years ago
rahel14350
▴ 10
0
votes
0
replies
1.3k
views
Can't get the lumi and methylumi packages to work.
lumi
methylumi
6.9 years ago
gitteba
• 0
2
votes
4
replies
2.6k
views
Problem in installing Bioconductor packages due to "IRanges"
lumi
methylumi
methyAnalysis
6.3 years ago
topijush
▴ 10
0
votes
0
replies
688
views
Error when trying to read in idat files in methylumi
methylumi
450k
methylation
methylome
4.3 years ago
A
▴ 40
0
votes
2
replies
1.0k
views
Convert MethyLumiSet into RGChannelSet (Illumina EPIC methylation data)
methylumi
minfi
microarray
epic
4.0 years ago • updated 3.5 years ago
Nala
• 0
0
votes
1
reply
1.5k
views
MethylSet to MethyLumiSet
minfi
methylumi
watermelon
7.2 years ago
Tom
▴ 10
43 results • Page
1 of 1
Recent ...
Replies
Comment: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
by
James W. MacDonald
65k
Both `RUVseq` and `sva` are meant to be used to remove technical variability. The problem is the identification of variability that is tech…
Comment: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
by
Alexandre
• 0
Hello James, Thank you very much for your answer and taking the time to read my post. I understand your remark, but isn't the approach o…
Comment: PCA plot suggestions
by
JKim
• 0
cross post: https://www.biostars.org/p/9593486/
Answer: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
by
James W. MacDonald
65k
You cannot correct for technical variability due to batch if samples are nested in batch. The technical and biological differences are comp…
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2)
by
James W. MacDonald
65k
You will need to show some reproducible code for anybody to track this down. Please note that `DESeq2` has been used by thousands of people…
Votes
Answer: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
Answer: Use of negative binomial model for exponential decay rate estimation using DESeq
C: null model and DEXSeqDataSet object in DEXSEQ
A: Are published RNA seq data analyses often wrong in calculating p-values and FDR?
A: How to explain how DESeq2 works to someone with zero bioinformatics background?
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