Log In
Sign Up
about
faq
Ask a question
Latest
News
Jobs
Tutorials
Tags
Users
New Post
Latest
News
Jobs
Tutorials
Tags
Users
Log In
Sign Up
About
Limit
all time
today
this week
this month
this year
Unanswered
All posts
Sort
Update
Answers
Bookmarks
Creation
Replies
Rank
Views
Votes
Showing :
ChAMP
•
reset
0
votes
3
replies
157
views
methylated/unmethylated media threshold (EPIC assay)
IlluminaHumanMethylationEPICanno.ilm10b3.hg19
ChAMP
minfi
7 weeks ago • updated 4 days ago
ramonfallon
• 0
0
votes
1
reply
49
views
champ.SVD() error, assumes standard class() function will return single string
ChAMP
updated 4 days ago by
Basti
▴ 280 • written 4 days ago by
ramonfallon
• 0
0
votes
4
replies
184
views
ERROR happens when install "DSS" package
methylationArrayAnalysis
ChAMP
DMP
DSS
9 days ago • updated 8 days ago
16301050225
• 0
0
votes
4
replies
145
views
Problem installing ChAMP package.
ChAMP
4 weeks ago
Yu-min
• 0
0
votes
1
reply
93
views
How to control for confounders in champ.DMP and champ.DMR?
ChAMP
updated 6 weeks ago by
Basti
▴ 280 • written 6 weeks ago by
l.milicic
• 0
0
votes
1
reply
138
views
Error in ChAMP GUI
ChAMP
shiny
ChAMPdata
updated 9 weeks ago by
anna.stanislawska
• 0 • written 10 weeks ago by
Mari
• 0
0
votes
1
reply
291
views
Error using ChAMP SVD analysis
ChAMP
updated 4 months ago by
behr201
• 0 • written 10 months ago by
FWNL15
• 0
0
votes
0
replies
161
views
Error in champ.svd - function 'EstDimRMTv2' within champ.svd acting inconsistently?
minfiData
ChAMP
4 months ago
behr201
• 0
0
votes
3
replies
309
views
Wrong terminology used on champ.load() output of ChAMP package?
ChAMPdata
ChAMP
updated 5 months ago by
Basti
▴ 280 • written 5 months ago by
mariat
• 0
0
votes
0
replies
223
views
Problem loading Red channel idat files with champ.load
R
MethylationArrayData
ChAMP
5 months ago
Paulina
• 0
0
votes
3
replies
2.1k
views
Problem loading R packages on MacBook Pro
newpackage
ChAMP
updated 4 weeks ago by
AmyB
• 0 • written 6 months ago by
Brendon
• 0
0
votes
2
replies
203
views
problems opening ChAMP
ChAMP
updated 6 months ago by
Basti
▴ 280 • written 6 months ago by
AaVee
• 0
0
votes
1
reply
245
views
error in champ.norm
champ.norm
ChAMP
updated 7 months ago by
Kevin Blighe
3.5k • written 7 months ago by
yu
• 0
0
votes
0
replies
197
views
ChAMP.CNA analysis
CopyNumberPlots
ChAMP
CopyNumberVariation
CopyNumberVariationData
8 months ago
FWNL15
• 0
0
votes
2
replies
364
views
Why the order of sample names in the beta matrix affect the analysis results of Champ.DMP? What should I do?
ChAMP
limma
Bioconductor
ChAMPdata
9 months ago • updated 8 months ago
Jinyue
• 0
0
votes
5
replies
373
views
Loading ChAMP IdatFiles with two different ArrayTypes
ChAMP
updated 9 months ago by
Yuan Tian
▴ 250 • written 10 months ago by
FWNL15
• 0
0
votes
6
replies
851
views
Merge problems in R
methylationArrayAnalysis
ChAMP
MethylationArrayData
10 months ago
FWNL15
• 0
1
vote
1
reply
263
views
How to solve the error in running champ.DMP()
ChAMP
updated 12 months ago by
Basti
▴ 280 • written 12 months ago by
Federica
▴ 10
2
votes
1
reply
276
views
How to save results of each step from ChAMP pipeline?
Bioconductor
ChAMP
updated 12 months ago by
Yuan Tian
▴ 250 • written 12 months ago by
Federica
▴ 10
2
votes
1
reply
312
views
How to download the ChAMP dependency ChAMPdata
ChAMP
ChAMPdata
updated 12 months ago by
shepherl
3.1k • written 12 months ago by
Federica
▴ 10
0
votes
2
replies
397
views
champ.SVD() : Error in while (step == 0) { : missing value where TRUE/FALSE needed
methylationArrayAnalysis
EPICarray
ChAMP
Champ.SVD
13 months ago
arisarkar88
• 0
0
votes
1
reply
328
views
Trouble Loading Data into Champ
loaddata
ChAMPdata
champload
R
ChAMP
updated 15 months ago by
Basti
▴ 280 • written 15 months ago by
Bethan
• 0
0
votes
2
replies
379
views
Error myDMP not found
Illumina
methylationArrayAnalysis
ChAMPdata
ChAMP
15 months ago
sissialva21
• 0
0
votes
11
replies
3.8k
views
ChAMP input: Beta Matrix?
champ
dmr analysis
updated 16 months ago by
坤
• 0 • written 6.2 years ago by
Shicheng Guo
• 0
0
votes
0
replies
216
views
ChAMP batch effect
ChAMP
17 months ago
SMA180043
• 0
1
vote
2
replies
422
views
what is "sample_well" and "pool_ID" in ChAMP
ChAMP
17 months ago
Hongbii
• 0
1
vote
6
replies
990
views
Blood cell composition adjustment in methylation EPIC array: ChAMP
MethylationArray
methylationArrayAnalysis
ChAMP
updated 6 weeks ago by
l.milicic
• 0 • written 17 months ago by
Ankit
▴ 10
3
votes
4
replies
668
views
Why the LogFC and delta-beta value are different in ChAMP
DNAMethylation
ChAMP
17 months ago
Hongbii
• 0
1
vote
1
reply
260
views
champ.DMP finds different probes in A-vs-B and B-vs-A analysis
DifferentialMethylation
ChAMP
champ.DMP
updated 18 months ago by
Yuan Tian
▴ 250 • written 18 months ago by
Ricardo
• 0
1
vote
3
replies
977
views
normalization combination of noob + BMIQ/Quantile
minfi
bmiq
noob
preprocessQuantile
champ
updated 20 months ago by
James W. MacDonald
59k • written 20 months ago by
Lin
▴ 50
0
votes
1
reply
259
views
the function DMR in ChAMP package
ChAMP
DMR
updated 23 months ago by
Yuan Tian
▴ 250 • written 23 months ago by
olive8306
• 0
0
votes
6
replies
551
views
error with champ.load
ChAMP
champ
methylation
updated 9 months ago by
Nidhi
• 0 • written 2.1 years ago by
jkong
• 0
0
votes
1
reply
212
views
rebuild the ChAMP package
ChAMP
updated 2.1 years ago by
Martin Morgan
25k • written 2.1 years ago by
olive8306
• 0
0
votes
0
replies
178
views
ChAMP DMP col abbreviations stend for what?
ChAMP
2.1 years ago
julie
• 0
0
votes
1
reply
365
views
about the ChAMP package, the champ.norm output different results,when run it twice on epic data.
ChAMP
updated 2.2 years ago by
Yuan Tian
▴ 250 • written 2.2 years ago by
olive8306
• 0
1
vote
3
replies
497
views
Skewed beta-distribution from Methylation EPIC array data
ChAMP
EPIC
Illumina
Methylation
2.3 years ago
erwin.tomasich
▴ 10
1
vote
1
reply
306
views
Issue with ChAMP DMP.GUI
ChAMP
champ
methylation
EPIC
updated 2.3 years ago by
Yuan Tian
▴ 90 • written 2.3 years ago by
cherlyn.t
• 0
2
votes
16
replies
1.0k
views
Methylation EPIC array: ChAMP package-champ.load added probes?
methylation
epic
champ
champ.load()
Methylation array
updated 2.4 years ago by
Yuan Tian
▴ 250 • written 2.4 years ago by
Ankit
▴ 10
1
vote
2
replies
437
views
ChAMP not handling 3+ levels in contrasts
champ
updated 2.6 years ago by
Yuan Tian
▴ 250 • written 2.7 years ago by
ognjen011
• 0
0
votes
2
replies
500
views
cpg.annotate model requirements
DMRcate
ChAMP
updated 2.8 years ago by
Yuan Tian
▴ 250 • written 2.8 years ago by
kadm
• 0
0
votes
1
reply
949
views
Tutorial:
Differential Methylation Analysis using ChAMP
champ
Tutorial
updated 2.9 years ago by
Yuan Tian
▴ 250 • written 2.9 years ago by
learning.iq84
• 0
2
votes
4
replies
654
views
bumphunter stalls on "Smoothing coefficients"
bumphunter
ChAMP
updated 3.0 years ago by
Yuan Tian
▴ 250 • written 3.0 years ago by
rasmus.rydbirk
▴ 10
0
votes
1
reply
750
views
ChAMP::champ.norm Error in champ.BMIQ(beta[, x], design.v, sampleID = colnames(beta)[x], : task 1 failed - "only defined on a data frame with all…
ChAMP
methylation
BMIQ
updated 3.0 years ago by
Yuan Tian
▴ 250 • written 3.0 years ago by
moldach
▴ 20
2
votes
5
replies
1.1k
views
Error in Champ for Bioconductor performing GSEA analysis on Methlayion array data
champ
bioconductor
methyaltion
epic array
updated 3.3 years ago by
godai987654
• 0 • written 3.3 years ago by
erinkello
• 0
1
vote
8
replies
1.4k
views
Error in Champ for Bioconductor analyzing Methlayion array data
champ
bioconductor
contrastmatrix
compare.group
updated 3.4 years ago by
Yuan Tian
▴ 250 • written 3.4 years ago by
erinkello
• 0
1
vote
5
replies
1.1k
views
error while using champ.svd() function
champ
3.4 years ago
sinha.puja
▴ 10
0
votes
3
replies
804
views
ChAMP Methylation analysis error code "could not find function champ.load"
champ
3.4 years ago
sinha.puja
▴ 10
2
votes
1
reply
672
views
EPIC methylation array - analysis with ChAMP - how to export bed/wig file to view in UCSC/IGV?
methylation
epic
champ
updated 3.5 years ago by
Yuan Tian
▴ 250 • written 3.5 years ago by
D
• 0
0
votes
2
replies
502
views
How can I define which samples are controls and which samples are cases in ChAMP
ChAMP
champ.DMP
Cases
Controls
references
3.6 years ago
yuabrahamliu
• 0
0
votes
2
replies
838
views
Use ChAMP to Find Differential Methylation Regions (DMR)
ChAMP
DMR
champ.DMR
3.6 years ago
yuabrahamliu
• 0
50 results • Page
1 of 1
Recent ...
Replies
Comment: Transcript-level differential expression using DESeq2
by
Ekta
• 0
Ok.. thanks for your valuable suggestion and quick replies. I have generated an MA plot using plotMASwish. thanks ekta
Comment: Warnings when using "ashr" in lfcshrinkage for DESeq2
by
Michael Love
37k
Sorry, I haven't seen this. Maybe try filtering low count genes? ``` keep <- rowSums(counts(dds) >= 10) >= X dds <- dds[keep,] # then run …
Comment: Transcript-level differential expression using DESeq2
by
Michael Love
37k
To show some extent of the DTE you can plot the LFC of the significant set and their mean count, we have `plotMASwish` to do this. Another…
Comment: Transcript-level differential expression using DESeq2
by
Ekta
• 0
No, the Volcano plot is not essential. I just wanted to show DETs with the help of a plot. Could you suggest a way for it? What are the oth…
Comment: Warnings when using "ashr" in lfcshrinkage for DESeq2
by
andrebolerbarros
▴ 10
Hi Michael, I'm using the "contrast" parameter, so I cannot use apeglm with that, as far as I know. The "coef" will not allow me to do eve…
Votes
Comment: Transcript-level differential expression using DESeq2
Comment: Transcript-level differential expression using DESeq2
Answer: how to make a group to apply the data to CAMERA
Answer: how to make a group to apply the data to CAMERA
Comment: Using vegan::betadisper for determing if I subset my design for DESeq2
Awards
• All
Scholar
to
Gordon Smyth
45k
Popular Question
to
andrebolerbarros
▴ 10
Scholar
to
James W. MacDonald
59k
Scholar
to
Guido Hooiveld
★ 3.2k
Scholar
to
Kevin Blighe
3.5k
Locations
• All
United States,
3 minutes ago
WEHI, Melbourne, Australia,
11 minutes ago
V&A Waterfront, Cape Town, South Africa,
20 minutes ago
United States,
26 minutes ago
United Kingdom,
45 minutes ago
Traffic: 304 users visited in the last hour
Content
Search
Users
Tags
Badges
Help
About
FAQ
Access
RSS
API
Stats
Use of this site constitutes acceptance of our
User Agreement and Privacy Policy
.
Powered by the
version 2.3.6